Freesurfer October 2021

freesurfer@nmr.mgh.harvard.edu

81 participants
113 discussions

recon-all missing files
by Alireza Karami 27 Oct '21

27 Oct '21

External Email - Use Caution Hello I used the following command to create the surface of my subject: recon-all -s subj -i anat.nii -all -qcache -3T However, some files are missing for some subjects. The missing files are .asc files inside the surf folder and COR-001, COR-002, ... inside the orig folder in mri. I used the same command to create the surface of all subjects, but I do not know why the above files are missing for some of them. All the best, Ali

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ERROR: niiRead(): error opening file
by g.toniol＠libero.it 27 Oct '21

27 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, Thank you for your work ! I am trying to segment .nii images with FS, using an ubuntu shell in Windows 10. When I run the command "recon-all" I receive the Error message that the file "exists but is not readable". So I tried converting the file with mri_convert but the following error appears: "niiRead(): error opening file". I tried selecting several different .nii files from different subjects but the same errors appear, I think it is unlikely that all files are corrupted: what may be the cause? I am new to Freesurfer and I apologize if my question is naive but I cannot find a solution in any of the online resources. Thank you very much for your time! Best regards. ________ $ recon-all -s S001 -i /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii ERROR: /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii exists but is not readable $ mri_convert /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii S001/mri/orig/001.mgz ERROR: niiRead(): error opening file /usr/local/freesurfer/7-dev/ws44891-153636-00001-00192-1.nii

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Hard Failures with recon-all
by Wacker, Ewa Helene 27 Oct '21

27 Oct '21

External Email - Use Caution Hello FreeSurfer Developers, for my project I am using Freesurfer 7.1 to examine the hippocampal volumes of patients with major depressive disorder (and controls) using the automatic segmentation. Therefore I have ran recon-all on all the 242 subjects. 12 of them did exit with an ERROR in form of a hard failure. I had troubles finding enough information online on how I could try to fix them by myself. The reports state the following: * for 2 subjects " 3d Normalization pass: could not read source volume brain.mgz\00" - example is subject AIDAB_2017_T1 * for 9 "could not find enough control points" example is subject AIDAB_3097_T1 * for 1 "MRI_watershed Error: global Region of the brain empty" example is subject AIDAB_4007_T1 Is there any chance that there will be a way to include some of the subjects? If needed, I would be happy to send more recon-all.log files, I attached one of each group to this email. Thank you for your time and support, Best regards, Ewa Helene Wacker

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ALL atlas and FS-FAST
by stdp82＠virgilio.it 26 Oct '21

26 Oct '21

External Email - Use Caution Hi is possible to use the AAL for connectivity analysis with FS-FAST? How can I segment the subject GM according with the labels listed in the ALL atlas? Thanks

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Issue with study
by Sarkis, Rani A.,M.D.,M.SC. 26 Oct '21

26 Oct '21

Hello all, I have an issue with a study, and am wondering whether it can be fixed. Freesurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c I am getting a bad talairach output message and when I try to address it with tkregister2 it seems that the orientations are off with coronal sections being treated as sagittal. I assume there is an issue with acquisition. The raw data through freeview looks Ok. all the best, rani

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Converting volume to annotation
by Lorenzo Pini 25 Oct '21

25 Oct '21

External Email - Use Caution Dear experts, I created a modified version of aparc+aseg.mgz files. Values now represent the functional connectivity strength of each parcel in the Desikan-Killiany atlas (ranging from -0.2 to 1 - rvalues). I would like to represent these new parcellation r-values over the native inflated surface (with freeview maybe?). How can I convert this volume (modified aparc+aseg - in orig.mgz space) to label/annotation to be represented on the surface? Thanks!

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trouble accessing Allen Atlas recons
by Budhdeo, Sanjay 25 Oct '21

25 Oct '21

External Email - Use Caution Hi FreeSurfer community, I’m trying to download the Allen Brain Atlas surface reconstructions at this webpage: https://secure-web.cisco.com/17v_p574C0gbjPcUGcI-1oAdpOuTLVkcnkI9eEapnGbJob… Unfortunately I haven’t been able to the download the file. I’ve tried the following mitigation steps : - trying to download using (FreeSurfer v5.3 recons<ftp://surfer.nmr.mgh.harvard.edu/pub/data/AllenBrainFreeSurferv5.3.tar.gz>) in Safari and Firefox - using a home and university connection - using a download manager - using Cyberduck for ftp access to the file I’d be grateful for any advice on how to download the recons! Many thanks, Sanjay Budhdeo

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Re: [Freesurfer] long_mris_slopes
by Veena Nair 22 Oct '21

22 Oct '21

External Email - Use Caution That worked! *python2 /opt/softwarepackages/freesurfer/bin/long_mris_slopes --qdec qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time months --qcache fsaverage --sd $SUBJECTS_DIR* Thank you!

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long_mris_slopes
by Veena Nair 22 Oct '21

22 Oct '21

External Email - Use Caution Hello, I am trying to do some preliminary analysis of a longitudinal dataset, following the tutorial. I am running FS on Ubuntu 20.04 and freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c I have finished processing the dataset; to prepare the data for the statistical analysis, I am running this command. long_mris_slopes --qdec long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pcl --do-spc --do-stack --do-label --time years --qcache fsaverage --sd $SUBJECTS_DIR But I get the following error- File "/opt/softwarepackages/freesurfer/bin/long_mris_slopes", line 448 print '\nERROR: Specify --qdec (and other required arguments)\n' ^ SyntaxError: invalid syntax I tried (as sudo) fixing the typo in the script, but that didn't help!! I tried switching from python version 3 to 2 [a previous post on this issue had recommended the solution], but that didn't help. I would appreciate any inputs on how to fix this issue. Thank you.

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Re: [Freesurfer] [EXTERNAL] Re: Tracula 7.2 -bedp error
by Chong, Catherine (Cat), Ph.D. 21 Oct '21

21 Oct '21

External Email - Use Caution Dear Tracula Team, I ran the command suggested below to merge the files: bedpostx_postproc.sh /path/to/your/tracula/dir/subjname/dmri But this did not seem to work unfortunately, here is the output. Removing intermediate files Creating identity xfm /usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 150: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory /usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 151: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory /usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 152: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory /usr/local/biotools/fsl/6.0.5/bin/bedpostx_postproc.sh: line 153: /research/labs/neurology/cat/freesurfer/subjects/Tracula/DODHC09_1_out/dmri.bedpostX.bedpostX/xfms/eye.mat: No such file or directory Done From: <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of "Yendiki, Anastasia" <AYENDIKI(a)mgh.harvard.edu> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Date: Thursday, October 21, 2021 at 5:06 PM To: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Re: [Freesurfer] Dracula 7.2 -bedp error Not sure why, could be a specific version of FSL. You can try running the step that merges everything separately: bedpostx_postproc.sh /path/to/your/tracula/dir/subjname/dmri On a separate note: I have to do some emergency travel so I will not be monitoring the list through the next week. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of Chong, Catherine (Cat), Ph.D. <Chong.Catherine(a)mayo.edu> Sent: Thursday, October 21, 2021 6:16 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Dracula 7.2 -bedp error External Email - Use Caution Dear Tracula team, I am running 7.2 on a computing cluster and the -prep stage completes without error. The dmri directory show the following files, below. However, after running the second step ( -bedp), the files under dmri.bedpostX do not appear to have merged. (bvals bvecs cancel commands.txt diff_slices logs monitor xfms). I am not able to find any error messages and the bedpostx_post.o529573 log is below. I have also attached my script to the very bottom. I would be grateful for your guidance in helping me solve this problem. Cat Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value -n <N> : only use volume <N> from each input file (first volume is 0 not 1) Usage: fslmerge <-x/y/z/t/a/tr> <output> <file1 file2 .......> [tr value in seconds] -t : concatenate images in time -x : concatenate images in the x direction -y : concatenate images in the y direction -z : concatenate images in the z direction -a : auto-choose: single slices -> volume, volumes -> 4D (time series) -tr : concatenate images in time and set the output image tr to the final option value -n <N> : only use volume <N> from each input file (first volume is 0 not 1) Removing intermediate files Creating identity xfm Done ~ brain_anat_mni.nii.gz data_slice_0018.nii.gz data_slice_0042.nii.gz dcminfo.dat lowb_brain.nii.gz nodif_brain_mask_slice_0021.nii.gz nodif_brain_mask_slice_0045.nii.gz brain_anat.nii.gz data_slice_0019.nii.gz data_slice_0043.nii.gz dtifit_FA.nii.gz lowb.nii.gz nodif_brain_mask_slice_0022.nii.gz nodif_brain_mask_slice_0046.nii.gz brain_anat_orig.nii.gz data_slice_0020.nii.gz data_slice_0044.nii.gz dtifit_L1.nii.gz nodif_brain_mask.nii.gz nodif_brain_mask_slice_0023.nii.gz nodif_brain_mask_slice_0047.nii.gz bvals data_slice_0021.nii.gz data_slice_0045.nii.gz dtifit_L2.nii.gz nodif_brain_mask_slice_0000.nii.gz nodif_brain_mask_slice_0024.nii.gz nodif_brain_mask_slice_0048.nii.gz bvecs data_slice_0022.nii.gz data_slice_0046.nii.gz dtifit_L3.nii.gz nodif_brain_mask_slice_0001.nii.gz nodif_brain_mask_slice_0025.nii.gz nodif_brain_mask_slice_0049.nii.gz data.nii.gz data_slice_0023.nii.gz data_slice_0047.nii.gz dtifit_MD.nii.gz nodif_brain_mask_slice_0002.nii.gz nodif_brain_mask_slice_0026.nii.gz nodif_brain_mask_slice_0050.nii.gz data_slice_0000.nii.gz data_slice_0024.nii.gz data_slice_0048.nii.gz dtifit_MO.nii.gz nodif_brain_mask_slice_0003.nii.gz nodif_brain_mask_slice_0027.nii.gz nodif_brain_mask_slice_0051.nii.gz data_slice_0001.nii.gz data_slice_0025.nii.gz data_slice_0049.nii.gz dtifit_S0.nii.gz nodif_brain_mask_slice_0004.nii.gz nodif_brain_mask_slice_0028.nii.gz nodif_brain_mask_slice_0052.nii.gz data_slice_0002.nii.gz data_slice_0026.nii.gz data_slice_0050.nii.gz dtifit_V1.nii.gz nodif_brain_mask_slice_0005.nii.gz nodif_brain_mask_slice_0029.nii.gz nodif_brain_mask_slice_0053.nii.gz data_slice_0003.nii.gz data_slice_0027.nii.gz data_slice_0051.nii.gz dtifit_V2.nii.gz nodif_brain_mask_slice_0006.nii.gz nodif_brain_mask_slice_0030.nii.gz nodif_brain_mask_slice_0054.nii.gz data_slice_0004.nii.gz data_slice_0028.nii.gz data_slice_0052.nii.gz dtifit_V3.nii.gz nodif_brain_mask_slice_0007.nii.gz nodif_brain_mask_slice_0031.nii.gz nodif_brain_mask_slice_0055.nii.gz data_slice_0005.nii.gz data_slice_0029.nii.gz data_slice_0053.nii.gz dwi.bvals nodif_brain_mask_slice_0008.nii.gz nodif_brain_mask_slice_0032.nii.gz nodif_brain_mask_slice_0056.nii.gz data_slice_0006.nii.gz data_slice_0030.nii.gz data_slice_0054.nii.gz dwi.bvecs nodif_brain_mask_slice_0009.nii.gz nodif_brain_mask_slice_0033.nii.gz nodif_brain_mask_slice_0057.nii.gz data_slice_0007.nii.gz data_slice_0031.nii.gz data_slice_0055.nii.gz dwi.ecclog nodif_brain_mask_slice_0010.nii.gz nodif_brain_mask_slice_0034.nii.gz nodif_brain_mask_slice_0058.nii.gz data_slice_0008.nii.gz data_slice_0032.nii.gz data_slice_0056.nii.gz dwi_motion_byvol.txt nodif_brain_mask_slice_0011.nii.gz nodif_brain_mask_slice_0035.nii.gz nodif_brain_mask_slice_0059.nii.gz data_slice_0009.nii.gz data_slice_0033.nii.gz data_slice_0057.nii.gz dwi_motion.txt nodif_brain_mask_slice_0012.nii.gz nodif_brain_mask_slice_0036.nii.gz nodif_brain_mask_slice_0060.nii.gz data_slice_0010.nii.gz data_slice_0034.nii.gz data_slice_0058.nii.gz dwi.nii.gz nodif_brain_mask_slice_0013.nii.gz nodif_brain_mask_slice_0037.nii.gz nodif_brain_mask_slice_0061.nii.gz data_slice_0011.nii.gz data_slice_0035.nii.gz data_slice_0059.nii.gz dwi_orig.1.bvals nodif_brain_mask_slice_0014.nii.gz nodif_brain_mask_slice_0038.nii.gz nodif_brain_mask_slice_0062.nii.gz data_slice_0012.nii.gz data_slice_0036.nii.gz data_slice_0060.nii.gz dwi_orig.1.bvecs nodif_brain_mask_slice_0015.nii.gz nodif_brain_mask_slice_0039.nii.gz nodif_brain_mask_slice_0063.nii.gz data_slice_0013.nii.gz data_slice_0037.nii.gz data_slice_0061.nii.gz dwi_orig.1.nii.gz nodif_brain_mask_slice_0016.nii.gz nodif_brain_mask_slice_0040.nii.gz nodif_brain_mask_slice_0064.nii.gz data_slice_0014.nii.gz data_slice_0038.nii.gz data_slice_0062.nii.gz dwi_orig_las.bvals nodif_brain_mask_slice_0017.nii.gz nodif_brain_mask_slice_0041.nii.gz nodif_brain_mask_slice_0065.nii.gz data_slice_0015.nii.gz data_slice_0039.nii.gz data_slice_0063.nii.gz dwi_orig_las.bvecs nodif_brain_mask_slice_0018.nii.gz nodif_brain_mask_slice_0042.nii.gz xfms data_slice_0016.nii.gz data_slice_0040.nii.gz data_slice_0064.nii.gz dwi_orig_las.nii.gz nodif_brain_mask_slice_0019.nii.gz nodif_brain_mask_slice_0043.nii.gz data_slice_0017.nii.gz data_slice_0041.nii.gz data_slice_0065.nii.gz dwi_snr.txt nodif_brain_mask_slice_0020.nii.gz nodif_brain_mask_slice_0044.nii.gz ! /bin/bash #$ -N recon-all #$ -cwd #$ -o /research/ freesurfer/logs_$TASK_ID #$ -e /research/ /freesurfer/logs_$TASK_ID #$ -j y #$ -M xx(a)mayo.edu #$ -m abe ###$ -pe threaded 4 #$ -notify #$ -l h_vmem=20G #$ -V #$ -l h_stack=20M #$ -t 1 set -x curr_subj=$(sed -n "${SGE_TASK_ID}p" /research/labs/neurology/cat/freesurfer/subjects/subject_list3) echo $curr_subj export FREESURFER_HOME=/usr/local/biotools/freesurfer/freesurfer-v7.2.0 export SUBJECTS_DIR=/research/labs/neurology/cat/freesurfer/subjects source $FREESURFER_HOME/SetUpFreeSurfer.sh export FSLDIR="/usr/local/biotools/fsl/6.0.5/" source ${FSLDIR}/etc/fslconf/fsl.sh export PATH="${FSLDIR}/bin:${FREESURFER_HOME}/bin:$PATH" export FSLDIR PATH unset PROFILE cat > config << END set dtroot = $SUBJECTS_DIR/Tracula set subjlist = DODHC09_1_out set dcmroot = $SUBJECTS_DIR/$curr_subj set dob0 = 0 set doeddy = 1 set interreg = 1 END trac-all -path -i $SUBJECTS_DIR/$curr_subj/IM-0003-0001.dcm -subject ${curr_subj} -c config

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Freesurfer October 2021