Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30083 discussions

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

2 1

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!

2 1

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

1 0

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!

1 0

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.

2 1

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

1 0

Using only a aparc+aseg input file for TRACULA
by Alexopoulos, Dimitrios 21 Oct '21

21 Oct '21

External Email - Use Caution Hi, It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the segmentation labels in the aparc+aseg. Is this correct? How would we run trac-all if we only had an aprc+aseg from another pipeline that generates FS-compatible outputs? For example, trac-all -preproc -bedp -path -c (where c = dmrirc config file). Jim ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.

3 9

Dracula 7.2 -bedp error
by Chong, Catherine (Cat), Ph.D. 21 Oct '21

21 Oct '21

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

2 1

Re: [Freesurfer] developer password of Freesurfer VBOx
by fsbuild 20 Oct '21

20 Oct '21

External Email - Use Caution Sending the info to your email shortly. - R. On Oct 20, 2021, at 11:11, byu <byu(a)cmu.edu.cn> wrote:        External Email - Use Caution        I am radiologist of Shengjing hospital of China Medical University. I am now  attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it requests a login password for the "Developer" account. Would you be able to provide a password please?Thanks！Bing Yubyubyu@cmu.edu.cn签名由网易邮箱大师定制_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Re: [Freesurfer] developer password
by fsbuild 20 Oct '21

20 Oct '21

External Email - Use Caution Sending the info to your email shortly. - R. On Oct 20, 2021, at 10:31, Joshua Ericson <josheric(a)hssdschools.org> wrote:        External Email - Use Caution        I am attempting to start Freesurfer - Ubuntu via VirtualBox on Windows 10, but it requests a login password for the "Developer" account, while installation guide assumes automatic login. Would you be able to provide a password please?Joshua Ericson Technology EducationBay Port High School_______________________________________________Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

1 0

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer