Retrospective tagging

[oesteban]

It would be nice to enable tagging (I do not know who would be the appropriate role) after new conversation has been posted.

In practice, I would like to add the “fmriprep” tag to these conversations:

Fmriprep/nipype error in docker://fmriprep:latest?

I’m not sure if this is a user-error or a fmriprep error. Any thoughts would be welcome. Thanks, Todd Running fmriprep through singularity as follows: singularity exec -B $base:/mnt -B $scratch:/workdir -c docker://poldracklab/fmriprep fmriprep $DATADIR $OUTDIR participant --participant_label $subject --nthreads 8 –mem_mb 10000 --ignore slicetiming -w $WORKDIR I get some nipype errors of the following flavor: 171009-18:22:26,590 workflow INFO: Executing node summary in dir: /workdir/fm…

Missing 001.mgz using fmriprep 1.0.8

I was using fmriprep 1.0.8 on sherlock to preprocess some functional and anatomical scans but couldn’t set up the original anatomical scan for freesurfer. Any thoughts will be appreciated! Thanks! and got the following error report: Traceback (most recent call last): File “/usr/local/miniconda/bin/fmriprep”, line 11, in load_entry_point(‘fmriprep==1.0.8’, ‘console_scripts’, ‘fmriprep’)() File “/usr/local/miniconda/lib/python3.6/site-packages/fmriprep/cli/run.py”, line 267, in main fmripre…

FMRIPREP on cluster?

Hi, I’m using FMRIPREP with fmriprep-docker on my local Mac machine but it’s very slow. What is the preferred and suggested way to either use e.g. AWS or something else to scale this up and make it run faster? With thanks

Fmriprep v1.0.12 hanging

Hi experts, I am attempting to update from v1.0.3 to v1.0.12 of fmriprep and I’m hitting a snag. I wanted to reach out to see if anyone has encountered this issue before. Due to the constraints of our cluster, I’m working from a manually prepared environment. Things work fine with v1.0.3, but things appear to stall during processing when I try to run v1.0.12 (which is set up in a separate environment). I’m trying both versions on the same test data set. I’ve saved the workflow output for the su…

Fixing inconsistent output spaces across studies in fmriprep 1.0.6

Hi, all. We’re trying to combine data from several different scanners using different acquisition sequences with differing voxel sizes. Obviously, this is a problem with the default parameters from fmriprep because the output MNI maps maintain the original voxel dimensions. If I understand correctly, I can standardize the fmriprep outputs using the --output-grid-reference flag. I could use help with two questions concerning this: Which resolution should I choose? I can imagine arguments for …

Creating Tiled Montage with nilearn

I have started using nilearn and its plotting capabilities to create beautiful images. I have been using plotting.plot_stat_map function, which is working very well for most of my needs. When trying to plot a large number of slices (>7) the images are concatenated from left to right. Ideally, I would like to specify the number of rows and columns where the images should be placed. At the moment, I am saving each image individually and then creating a montage with ImageMagick. If anyone has a…

Fmriprep : last release (18th of July 2017) not on Sherlock

Hi all, I would like to preprocess my data with the latest release of fmriprep and it seems to be a release the 18th of July 2017 according to https://fmriprep.readthedocs.io/en/stable/ Does someone have an idea where to found it on Sherlock server ? ( I have been to the following path /share/PI/russpold/singularity_images/ but was unable to see it). Thank you, Regards, Redwan

Fmriprep normalization with ANTs, transformation matrix

Hi, I’ve run the fmriprep workflows using all the default settings on a dataset that includes both anatomical and functional images, with the only changes being “no freesurfer”, and I required fmri output in both native space and in MNI. I have all the output now with slightly modified versions of the bold_space_T1w_preprocess images where I regressed out the confound estimates and kept only the residuals from that regression. Ideally I would like to run nilearn spotlight analyses on this data…

Latest versions fmriprep did not finish openFMRI dataset ds000164 on openneuro.org

Hey guys, I noticed that for the openFMRI dataset ds000164 (https://openneuro.org/datasets/ds000164/versions/00001), the fmriprep containers only processed subject 1 (for fmriprep 1.0.15) or subject 1-3 (1.0.14). Anyone an idea what went wrong here? Cheers, Gilles

FMRIPREP autorecon31 error

Hello, I’m processing some data with FMRIPREP v 1.0.3 and have hit an error for a subset of the subjects. I’ve pasted the start of the error log below and saved a sample report here: https://www.dropbox.com/s/5xtpamkugfe5xhq/example.pdf?dl=0. I believe that there is an issue with one of the Freesurfer steps, but I’m not quite sure where to begin in debugging the issue since I have no experience with Freesurfer prior to using FMRIPREP (and I’m still relatively new to the latter). Processing comp…

Fmriprep install issues

Hi Neurostars! I’m working with my local IT folks to get fmriprep up and running, which is very exciting. There’s an odd behavior, though. When I try to load the module in python there are errors implying modules are missing, but they aren’t. Below is a screen cap of the error I’m getting, but I can run this successfully from nilearn.masking import compute_epi_mask and that seems to be the “problem”. Thanks for any help! Jeanette [image]

Niworkflows: appropriate for non-fmriprep developers/pipelines?

Hey, I guess this is for @effigies and @ChrisGorgolewski I am very curious about the ‘niworkflows’-project. This seems to have some very nice features on top of nipype. For example, you can make ‘hooks’ that draw nice HTML reports for a given node. This is something that would be very useful in my own project, where I am setting up a workflow for laminar-resolved fMRI at UHF (fmriprep doesn’t cut it there for me). However, I also notice niworkflows contains a new branch of the Nipype engine t…

Trouble with html report for fmriprep v1.0.3

Hello, I’m a relatively new user of fmriprep, which I have found to be fantastic so far. I’ve been working with IT support at my school to upgrade from v0.6.6 to v.1.0.3 on our cluster. We were able to get v0.6.6 to work after a bit of trial-and-error, but we’re hitting a snag with v.1.0.3. Specifically, while it seems as though all of the processing steps may be running correctly with v.1.0.3, we have not been able to get the html report to be generated properly. At first, it looked like we we…

FMRIPREP: Susceptibility distortion/Fieldmap problems

Hi, I was just running FMRIPrep on my data and all is working fine as long I do not realized the fieldmap correction. Here is an example output: https://www.dropbox.com/s/yqei7d2q212jeir/sub-AKA01.pdf?dl=0 First I expected the correction did not work since my phase data was stored from -2pi to +2pi but I know also tryed 0 to +4pi and 0 to +2pi. Unfortunately I could not find a description how the field map data should be coded. here is also the phase image and the corresponding .json file: ht…

Will fmriprep slice timing correction work for my multiband slice timing?

Hi all, I have the following slice timing for my multiband data : [ 0, 0.0775, 0.1575, 0.2375, 0.315, 0.395, 0.475, 0.5525, 0.6325, 0.7125, 0.79, 0.87, 0.95, 1.0275, 1.1075, 1.1875, 1.265, 1.345, 1.425, 1.5025, 1.5825, 1.6625, 1.74, 1.82, 1.9, 0, 0.0775, 0.1575, 0.2375, 0.315, 0.395, 0.475, 0.5525, 0.6325, 0.7125, 0.79, 0.87, 0.95, 1.0275, 1.1075, 1.1875, 1.265, 1.345, 1.425, 1.5025, 1.5825, 1.6625, 1.74, 1.82, 1.9, 0, 0.0775, 0.1575, 0.2375, 0.315, 0.395, 0.475, 0.5525, 0.6325, 0.7125, 0…

FMRIPREP work_dir outputs

Hi all, This may be painfully obvious, but how does fmriprep store all the processing outputs into work_dir in the organized way where each workflow/node inherits the working directory of the parent? I was playing around with nipype here and the top level workflow directory nuisance_regression_wf is in the right spot, but the other sub-workflows pop up in the directory I run the script from and all the nodes execute in /tmp. More pointedly, how do I get workflows/nodes to inherit base_dir have …

Fmriprep advices for multiband

Hi guys, The data has been collected for a very well known task and I am very surprised that at the 2nd level analysis I do not see anything. I would like to know by any chance if someone has some advice about the best way to preprocess multiband data. Am I removing too much signal during the preprocessing ? Am I not using the good preprocessing steps ? My data is multiband (Simultaneous Multi-Slice) with : TR = 400ms Number of frames = 876 Number of slices in one volume := 48 With fmripr…

BIDS and fmriprep: should I use my SBRef as inplane?

Hi, Each of my functional scans (acquired from a Simenese Prisma scanner) have an associated SBRef scan as well. Usually, before using BIDS, I used these as inplane images for registration and normalization. I noted that in the BIDS format there is both an option to include SBRef images in the functional directory, as well as an inplane image in the anatomy directory. I was wondering, in addition to including my SBRef in the functional directory, should I also use one of them as an inplane im…

Slice time correction in fmriprep

Hi all Many thanks for version 0.3.2 However, I’ve seen that the slice time correction (#415) is optional. With --ignore I can only ignore slicetiming but how to activate ? thanks!

Directory permissions issue

Hello, I am running fmriprep-docker on remote computer and I do not have ROOT permissions. However, it looks like the output directories (fmriprep and fresurfer) has only ROOT permission. Is there any way to change the output files permission so that the user has the ownership?

Need to downsample one nifti - how should i edit the JSON file?

hi all, i have one functional scan which was taken at a higher resolution than the rest, which i would like to use in analysis. i have been able to downsample it to the right resolution using freesurfer mri_convert, but now i am wondering what I should do in terms of making this BIDS compatible. i though i’d save the original volume as “sub-04_task-func_run-01_bold_2mm_orig.nii.gz” and the appropriately downsampled volume as “sub-04_task-func_run-01_bold.nii.gz”, to match the rest of the same-…

Events.tsv duration for block analysis

Hello, I am not sure how “events.tsv” files are being use in fmriprep-pipeline. I have three column like: onset duration type 30.0 1 1back 85.1 1 2back, However, later on at GLM, I am interested on using AFNI TENT function /block glm and in this case duration would not be 1. Should I re-run the full-fmriprep pipeline again with those change on “events.tsv” ? Or how it works incase of mix-design (regressing both -events and blocks ). Thanks BL

PhaseEncodingDirection

Hello, I was under the impression that we actually use epi_AP( A>P which is “j-“ ) (field maps) to perform distortion correction of BOLD_AP ( A>P , also "j-“). However, fmripep-pipeline ( https://fmriprep.readthedocs.io/en/0.4.4/sdc/unwarping.html) need opposing direction for this purpose. If so, in epi.JSON file of fieldmap_AP, at "IntendedFor” I should point the BOLD_image_PA (P>A, bold data collected with opposing phaseEncodingDirection)? please correct me if i am wrong. Could y…

Failed (exit code 1) on Sherlock server

Hi all, First I have used this following command line on Sherlock : singularity run /share/PI/russpold/singularity_images/poldracklab_fmriprep_0.3.1-2017-03-25-c38ac0136e8c.img /scratch/PI/aetkin/redwan/framing/sourcedata/ /scratch/PI/aetkin/redwan/preprocessed/ participant --participant_label sub-01 -w $LOCAL_SCRATCH After 40 hours, the preprocessing of only one subject was not done (with 64GB of ram and 16 cores per node) so I decided to kill the process. Then I have changed the command li…

Converting AFNI dataset to BIDS

Hi! I have an AFNI dataset that I converted to NIfTI using 3dAFNItoNIFTI. How can I make it a BIDS, in order to use fmriprep? Thank you, Carlotta.

Could not read error : while file ":/out/freesurfer/sub-001/mri/T2.prenorm.mgz" exist

Hello, Received following error almost at the end of the pipeline. Any idea why this could be ? Thanks BL … Applying LTAtransformInterp (resample_type 1) writing to /out/freesurfer/sub-001/mri/T2.prenorm.mgz… mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /out/freesurfer/sub-001/mri/aseg.presurf.mgz -surface /out/freesurfer/sub-001/surf/rh.white identity.nofile -surface /out/freesurfer/sub-001/surf/lh.white identity.nofile /out/freesurfer/sub-001/mri/T2.prenorm.mgz /out/fr…

Naming fieldmaps

To follow up on my “outside of the brain fMRI data” issue, I am trying to use phase field maps. For each run there are 2 phasic field maps. I also have two tasks, namely “CCD” and “loca”. I named the filed maps like ‘sub-01_task-CCD_run-02_phase1.nii.gz’, tried this on BIDS validator but got errors. I then renamed them to '‘sub-01_run-01_phase1.nii.gz’ and they worked well. But I am wondering, by naming filed maps like this, how would fmriprep know which filed maps correspond to which fMRI runs? …

Different scan direction

Hi, Can fmriprep handle different scan directions? i.e.- if some of the scans are top-down and some are vice versa- how should this be handled? Thanks!

Fmriprep / Docker: Error in ‘epi_to_t1w_transform’ and ‘epi_to_mni_transform’

Hi fmriprep users, We were intrigued by fmriprep and wanted to see if we can preprocess our MRI data with the pipeline. We have two runs for two tasks inside the scanner (total of 4 epi files) and a high-res structural (T1) scan. When setting everything up on a local machine, fmriprep (implemented via docker) worked really well, but since we moved to a cluster, we have not managed to get it to run through again. The error is not limited to a specific file, and trying the same starting command …

Thanks

[ChrisGorgolewski]

Admins can edit tags - I fixed the ones you listed.