Freesurfer

freesurfer@nmr.mgh.harvard.edu

6 participants
30091 discussions

slice timing
by Meryem Ayse Yucel 29 Mar '13

29 Mar '13

Hi, I am running a pASL sequence with a TR = 3 sec and TI2 = 1.8. I am wondering when I do slice time correction does that move all slices to the mid of TR that is 1.5 s prior in time or, it moves them to the timing of the mid slice, which would be the mid of image acquisition aorund 0.6 sec prior in time with respect to the end of TR. Thank you, Meryem

3 2

Use a SPM roi to extract thickness measurements
by McMains, Stephanie 29 Mar '13

29 Mar '13

Hi all, I have been trying to take an SPM volume and extract FS thickness measurements. I think I successfully took my spm volume from mni152 to fsaverage space (mni305) via the command line: mri_vol2vol --mov $FREESURFER_HOME/subjects/fsaverage/mri.2mm/mni305.cor.mgz --targ RTPJ_9mm_001_10_64_-54_16.img --reg $FREESURFER_HOME/subjects/fsaverage/mri.2mm/reg.2mm.mni152.dat --inv --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz Then I turned it into an ROI: mri_binarize --i $SUBJECTS_DIR/2506/mri/RTPJ_mni305_9mm_001_10_64_-54_16.nii.gz --o $SUBJECTS_DIR/2506/mri/RTPJ_mni305_roi_9mm_001_10_64_-54_16.nii.gz --min .0000000001 > From here I figured I could map it to the fsaverage surface (mri_vol2surf) and extract thickness measurements (mri_segstats using rh.thickness.fsaverage.mgh) as suggested in the volume roi cortical thickness workflow. However, some of my ROIs don't show up after I transform them. From what I can tell, this is because they don't intersect with the fsaverage surface. My thinking was that it might be better to stay within the individual subject space. So I would: 1. transform ROI to subject space 2. extract thickness values from rh.thickness However, I am struggling to get the roi into single subject space. I feel like this transform (or the inverse of it) should exist because I put all my subjects into fsaverage space via the -qcache flag, but i couldn't tell what to use. So I tried: fslregister --s 2506 --mov $SUBJECTS_DIR/fsaverage/mri/brainmask.mgz --reg $SUBJECTS_DIR/2506/fsaverage_to_indiv.dat But the registration doesn't look all that good. I am not sure if this is because the fsaverage is 'smoothed' or what. And then I am at a loss for how to put my roi into individual space and then extract thickness, or even if this is the right approach. Thanks, Stephanie

2 1

FS version of Colin27
by ZhiLiangLong 29 Mar '13

29 Mar '13

Hi FS experts: I am trying to map AAL template onto FS surface to create surface-based AAL template. Several days ago, i asked this question, and Garikoitz Lerma gave me some suggestions. Possibly, i think the process is like as folllows: 1. downloa the Colin27 subject in Surfrend page, and transform it to the latest FS version (5.2 currently). 2. obtain register.dat between Colin27 subject and single_subj_T1.nii under the canonical directory in SPM8 using bbregister. bbregister --s Colin27_subject --mov single_subj_T1.nii --reg register.dat --init-fsl --t1 3. transfrom each AAL ROI to the surface file with register.dat file obtained above using mri_vol2surf. mri_vol2surf --mov AAL_ROI.nii --reg register.dat --projdist-max 0 1 0.1 --interp nearest --hemi lh \ --out lh.Colin27_AALROI.mgh --reshape 4. use mri_label2label or mri_segstat to obtain the cortical thickness of each ROI for individual subject. My question is about the first step. How to transform the Colin27 subject to FS version 5.2? that is to say how can i get the FS version of Colin27 template instead of fsaverage template? Hope someone gives me some suggetions. Besh wishes.

2 1

selxavg3-sess problem with -per-run flag
by SHAHIN NASR 29 Mar '13

29 Mar '13

Hi, I used to run my mkanalysis-sess without indicating -per-run or -per-session, assuming that when I have pre-processed my files with -per-run flag then selxavg3-sess will do the same. But when I checked the analysis.info I noticed "PerSession 1" which I think it means system will use per-session preprocessing. So, this time I explicitly used -per-run in my mkanalysis-sess as below: preproc-sess -s <SubjId> -per-run -fwhm 5 -fsd bold -fwhm 5 -surf self rhlh mkanalysis-sess -analysis Reward.rh -surface self rh -native -fwhm 5 -paradigm Conds.par -event-related -polyfit 2 -gammafit 2.25 1.25 -mcextreg -TR 2.000 -nconditions 7 -refeventdur .10 -fsd bold -per-run -force This time when I ran selxavg3-sess command I faced this error: ERROR: cannot determine format of /autofs/cluster/tootell/pitcairn/1/shahin/Reward/Subjects/limi1/bold/004/fmcpr.sm5 (MRIread) Error in flac_customize (line 87) mri = MRIread(fstem,1); Error in fast_selxavg3 (line 65) flac0 = flac_customize(flac0); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n As I checked my subjects directory I had these files in /bold/004/ directory: fmcpr.nii.gz fmcpr.sm5.self.rh.nii.gz fmcpr.sm5.self.lh.nii.gz Notably, if I drop that -per-run flag from my mkanalysis-sess then system works without any problem. But then I am not sure whether I have processed my data in per-run or per-session mode. Any help will be appreciated Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] bbr problem run
by Anastasia Yendiki 29 Mar '13

29 Mar '13

Hi Sal - Would it be possible for you to run the bbregister command that fails (you can find the command line in trac-all.log) using both the 5.1 and 5.2 version of bbregister and see if one of them works on your system? a.y On Fri, 29 Mar 2013, Salil Soman wrote: > Hi Anastasia, > > Because I did not have a compatible older version of fsl on the SGE, I was not able to > run tracula with 5.1. > > Thank you, > > Sal > > > On Fri, Mar 29, 2013 at 8:32 AM, Anastasia Yendiki <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > > Hi Sal - Had you ever tried running this in 5.1? Just trying to figure out > if it's 5.2-specific. > > Thanks, > a.y > > On Thu, 28 Mar 2013, Salil Soman wrote: > > Thank you for your response. > I tried re-running Tracula using bbr in a subject I had > successfully run using flt. > trac-all prep and bedp worked without an error. Bedpostx sent > me an email confirming > bedpost completed without problem. However, when I try to run > trac-all paths, I get > the following error: > > Loading atlas reference volumefrom/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr > _end > 1_dil.nii.$ > niiRead(): error openingfile/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr > _end > 1_dil.nii.gz > ERROR: Could notread/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr > _end > 1_dil.nii.gz > > recon-all did finish without error. > > Best wishes, > > -S > > > On Thu, Mar 28, 2013 at 8:43 AM, Anastasia > Yendiki <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Sal, > > 1. I have no experience with the sun grid engine, > perhaps someone else on > the list can help with that. > > 2. The -bedp step needs the outputs from the -corr and > -masks steps. The > -path step needs the outputs from the -bedp step. The > output files from > each part are listed here: > > http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles > > 3. Checking the aparc+aseg should be enough for tracula > purposes as well, > since that's the freesurfer output that tracula uses. > Keep in mind that > DWI resolution is usually lower than T1 resolution, > so tiny changes in > the aparc+aseg might not affect tracula at all. > > 4. Yes, I do recommend using bbregister. It's not > surprising that it would > give better results since it uses the additional > information of the > surfaces. If I remember correctly, Doug didn't manage > to replicate your > bbregister error, right? I'd check if you get the > same error with the > 5.1 version of bbregister. > > Hope this helps, > a.y > > On Wed, 27 Mar 2013, Salil Soman wrote: > > Hi, > I have been able to implement FS 5.2 on our Sun > Grid Engine > Cluster using the CentOS 6 > distribution. After modifying the fsl_sub_mgh file > to work > with out cluster queue > names and to modify the email notifications, I am > able to run > the entire processing > pipeline using FLT. (Everytime I try bbr I get > errors. I had > email doug about this but > have not heard any response). > > I am submitting the jobs to the cluster as follows > > recon-all -i ./*.nii -s WCA_0202_T1_FS > -nuintensitycor-3T > -nocanorm -openmp 50 > -hippo-subfields -all > trac-all -prep -no-isrunning -c > /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -bedp -no-isrunning -c > /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > trac-all -path -no-isrunning -c > > /mnt/glusterfs/salsoman/SRC/WCA_0202_T1/DTI/dmrirc > > There are a few issues I am trying to sort out: > > 1) how should one conifigure the openmp flag for > the Sun Grid > Engine? the flag I used > did not change processing time, and each subject > is still > taking ~24 hrs? > > 2) once the script starts bedpost, bedpost has > controller code > which paralelizes all > of the slices (which has been great going from 12 > hrs of > processing to 1.5 hrs). > However, my original script goes on to execute > trace-all -path > ... before bepost is > done, generating errors. I have gotten around this > by running > the trace-all -path > command again after bedpost sends me an email > confirming > completion. Is there a way to > more cleanly do this (some kind of hold command I > can do based > on output from > bedpost)? > > 3) In your experience, how important is quality > control of > freesurfer on tracula > results? We have come to the compromise for > freesurfer output > to manually check the > segmentation of aparc+aseg.mgz using free view, > only > correcting and rerunning steps of > freesurfer when there are specific structures we > want the > volumes of (eg hippocampus). > > 4) have you found a significant benefit of bbr > over flt? If > so, any suggestions on > things I may need to check to get bbr to work > (given flt > works)? > > Best wishes, > > Sal > > > > > > > > > The information in this e-mail is intended only for the person > to whom it is > addressed. If you believe this e-mail was sent to you in error > and the e-mail > contains patient information, please contact the Partners > Compliance HelpLine at > http://www.partners.org/complianceline . If the e-mail was > sent to you in error > but does not contain patient information, please contact the > sender and properly > dispose of the e-mail. > > > > > >

2 1

mris_preproc with --xhemi
by Ejoe Yizhou Ma 29 Mar '13

29 Mar '13

Hi freesurfer experts, I'm investigating lh-to-rh asymmetry and am following instructions on this page :http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi. My question is, what does the "--xhemi" flag do in the "mris_preproc" command? It seems to me that it calculates (lh-rh) value at each vertex for every subject. (I tried to use the same subject for each pair of input for "--paired-diff", and the result is not a all-zero output.) It would also be nice if someone can tell me how to realize my final goal, which is to get the (lh-rh)/[(lh+rh)/2] value at each vertex for each subject in a .mgh file. Thanks, Cherry

2 2

Re: [Freesurfer] bbr problem run
by Salil Soman 29 Mar '13

29 Mar '13

Thank you for your response. I tried re-running Tracula using bbr in a subject I had successfully run using flt. trac-all prep and bedp worked without an error. Bedpostx sent me an email confirming bedpost completed without problem. However, when I try to run trac-all paths, I get the following error: Loading atlas reference volume from /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.$ niiRead(): error opening file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz recon-all did finish without error. Best wishes, -S On Thu, Mar 28, 2013 at 8:43 AM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Sal, > > 1. I have no experience with the sun grid engine, perhaps someone else on > the list can help with that. > > 2. The -bedp step needs the outputs from the -corr and -masks steps. The > -path step needs the outputs from the -bedp step. The output files from > each part are listed here: > http://www.freesurfer.net/**fswiki/trac-all#**Outputdirectoriesandfiles<http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles> > > 3. Checking the aparc+aseg should be enough for tracula purposes as well, > since that's the freesurfer output that tracula uses. Keep in mind that > DWI resolution is usually lower than T1 resolution, so tiny changes in > the aparc+aseg might not affect tracula at all. > > 4. Yes, I do recommend using bbregister. It's not surprising that it would > give better results since it uses the additional information of the > surfaces. If I remember correctly, Doug didn't manage to replicate your > bbregister error, right? I'd check if you get the same error with the > 5.1 version of bbregister. > > Hope this helps, > a.y > > > On Wed, 27 Mar 2013, Salil Soman wrote: > > Hi, >> I have been able to implement FS 5.2 on our Sun Grid Engine Cluster using >> the CentOS 6 >> distribution. After modifying the fsl_sub_mgh file to work with out >> cluster queue >> names and to modify the email notifications, I am able to run the entire >> processing >> pipeline using FLT. (Everytime I try bbr I get errors. I had email doug >> about this but >> have not heard any response). >> >> I am submitting the jobs to the cluster as follows >> >> recon-all -i ./*.nii -s WCA_0202_T1_FS -nuintensitycor-3T -nocanorm >> -openmp 50 >> -hippo-subfields -all >> trac-all -prep -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >> WCA_0202_T1/DTI/dmrirc >> trac-all -bedp -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >> WCA_0202_T1/DTI/dmrirc >> trac-all -path -no-isrunning -c /mnt/glusterfs/salsoman/SRC/** >> WCA_0202_T1/DTI/dmrirc >> >> There are a few issues I am trying to sort out: >> >> 1) how should one conifigure the openmp flag for the Sun Grid Engine? the >> flag I used >> did not change processing time, and each subject is still taking ~24 hrs? >> >> 2) once the script starts bedpost, bedpost has controller code which >> paralelizes all >> of the slices (which has been great going from 12 hrs of processing to >> 1.5 hrs). >> However, my original script goes on to execute trace-all -path ... before >> bepost is >> done, generating errors. I have gotten around this by running the >> trace-all -path >> command again after bedpost sends me an email confirming completion. Is >> there a way to >> more cleanly do this (some kind of hold command I can do based on output >> from >> bedpost)? >> >> 3) In your experience, how important is quality control of freesurfer on >> tracula >> results? We have come to the compromise for freesurfer output to manually >> check the >> segmentation of aparc+aseg.mgz using free view, only correcting and >> rerunning steps of >> freesurfer when there are specific structures we want the volumes of (eg >> hippocampus). >> >> 4) have you found a significant benefit of bbr over flt? If so, any >> suggestions on >> things I may need to check to get bbr to work (given flt works)? >> >> Best wishes, >> >> Sal >> >> >> >> >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline> . > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

2 2

Re: [Freesurfer] trac-all -path error
by Anastasia Yendiki 29 Mar '13

29 Mar '13

Hi Nawaf - The first error occured much earlier in the log file. Your gradient table file could not be found. Did you set the bvecfile variable in your configuration file? a.y On Fri, 29 Mar 2013, Nawaf Yassi wrote: > Hi Anastasia > Thanks for your reply > Here is the file attached (I have replaced the subject's name with 'AAAAA' > for anonymity) > Regards > Nawaf > > > On 29/03/13 2:17 AM, "Anastasia Yendiki" <ayendiki(a)nmr.mgh.harvard.edu> > wrote: > >> > Hi Nawaf - Can you please send your trac-all.log? It's possible that the >> > problem started at an earlier step. > > Thanks, > a.y > > On Thu, 28 Mar 2013, Nawaf >> Yassi wrote: > >> Dear mailing list >> >> I am encountering an error at the >> trac-all path stage of a tracula analysis (the >> first two stages on trac-all >> seem to have run ok) with the appropriate outputs. I am >> getting the error >> ³Segmentation fault² (core dumped) very early on after the >> dmri_paths >> command is run (see below). Can anyone help? >> >> I am using freesurfer 5.2 >> and FSL 5.0.2.1 (linux) >> Regards >> Nawaf >> ATTACHED: ERROR MESSAGE + config >> file below >> >> ========================================================= >> >> >> [nyassi@bee1 scripts]$ trac-all -path -c dmrirc_single_subject >> Too many >> )'s. >> INFO: SUBJECTS_DIR is >> >> /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> >> INFO: Diffusion root is >> >> /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> >> Actual FREESURFER_HOME /usr/local/freesurfer5.2 >> trac-paths >> -c/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C01 >> /scripts/ >> dmrirc.local >> -log/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C >> 01/scripts/ >> trac-all.log >> -cmd/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C >> 01/scripts/ >> trac-all.cmd >> #------------------------------------- >> >> /usr/local/freesurfer5.2/bin/trac-paths >> >> #------------------------------------- >> #@# Path reconstruction Thu Mar 28 >> 10:01:34 EST 2013 >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .cst_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .cst_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .ilf_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .ilf_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .unc_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .unc_AS_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/fm >> ajor_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/fm >> inor_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .atr_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .atr_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .ccg_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .ccg_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .cab_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .cab_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .slfp_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .slfp_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/lh >> .slft_PP_avg33_mni_bbr >> rm >> -rf/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/C0 >> 1/dpath/rh >> .slft_PP_avg33_mni_bbr >> /usr/local/freesurfer5.2/bin/dmri_paths >> --outdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf >> er/C01/dpath/lh >> >> .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/rh >> >> .cst_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/lh >> >> .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/rh >> >> .ilf_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/lh >> >> .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/rh >> >> .unc_AS_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/fm >> >> ajor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/fm >> >> inor_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/lh >> >> .atr_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/rh >> >> .atr_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/lh >> >> .ccg_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/rh >> >> .ccg_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/lh >> >> .cab_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/rh >> >> .cab_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis >> /C01_freesurfer/C01/dpath/lh >> >> .slfp_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysi >> s/C01_freesurfer/C01/dpath/rh >> >> .slfp_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysi >> s/C01_freesurfer/C01/dpath/lh >> >> .slft_PP_avg33_mni_bbr/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysi >> s/C01_freesurfer/C01/dpath/rh >> .slft_PP_avg33_mni_bbr >> --dwi/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ >> C01/dmri/dwi >> .nii.gz >> --grad/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> /C01/dmri/bve >> cs >> --bval/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> /C01/dmri/bva >> ls >> --mask/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> /C01/dlabel/d >> iff/lowb_brain_mask.nii.gz >> --bpdir/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfe >> r/C01/dmri.bed >> postX --ntr 2 --fmin 0.05 >> --roi1/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> /C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_end1_dil.nii.gz >> --roi2/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> /C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_end2_dil.nii.gz >> --reg/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ >> C01/dmri/xfm >> s/diff2mni.bbr.mat >> --init/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer >> /C01/dlabel/d >> >> iff/lh.cst_AS_avg33_mni_bbr_cpts_6.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.cst_AS_avg33_mni_bbr_cpts_6.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.ilf_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.ilf_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.unc_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.unc_AS_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/fmajor_PP_avg33_mni_bbr_cpts_7.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/fminor_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.atr_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.atr_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.ccg_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.ccg_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.cab_PP_avg33_mni_bbr_cpts_4.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.cab_PP_avg33_mni_bbr_cpts_4.txt/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.slfp_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.slfp_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.slft_PP_avg33_mni_bbr_cpts_5.txt/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.slft_PP_avg33_mni_bbr_cpts_5.txt >> --nprior/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf >> er/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Re >> covery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsnnids_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_fsnnprior_all/bilhome/nyassi/Imaging_Data/ANSWER-R >> ecovery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_fsnnids_all >> --lprior/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurf >> er/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cst_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ilf_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.unc_AS_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fmajor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/fminor_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.atr_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.ccg_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Reco >> very/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.cab_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recove >> ry/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov >> ery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slfp_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov >> ery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/lh.slft_PP_avg33_mni_bbr_fsids_all/bilhome/nyassi/Imaging_Data/ANSWER-Recov >> ery/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_fsprior_all/bilhome/nyassi/Imaging_Data/ANSWER-Rec >> overy/C01/Analysis/C01_freesurfer/C01/dlabel/m >> >> ni/rh.slft_PP_avg33_mni_bbr_fsids_all >> --seg/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ >> C01/dlabel/m >> ni/aparc+aseg.nii.gz --nb 200 --ns 7500 --nu 0 --nk 5 >> --sdp/bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/ >> C01/dlabel/d >> >> iff/lh.cst_AS_avg33_mni_bbr_cpts_6_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.cst_AS_avg33_mni_bbr_cpts_6_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.ilf_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.unc_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.unc_AS_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/fmajor_PP_avg33_mni_bbr_cpts_7_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/fminor_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.atr_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.atr_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.ccg_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.cab_PP_avg33_mni_bbr_cpts_4_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.cab_PP_avg33_mni_bbr_cpts_4_std.txt/bilhome/nyassi/Imaging_Data/ANSWER- >> Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.slfp_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/lh.slft_PP_avg33_mni_bbr_cpts_5_std.txt/bilhome/nyassi/Imaging_Data/ANSWER >> -Recovery/C01/Analysis/C01_freesurfer/C01/dlabel/d >> >> iff/rh.slft_PP_avg33_mni_bbr_cpts_5_std.txt >> Segmentation fault (core >> dumped) >> foreach: No match. >> >> >> ============================================================================== >> ======= >> ================================================ >> >> [nyassi@bee1 >> scripts]$ cat dmrirc_single_subject >> # >> # dmrirc.example >> # >> # This file >> contains commands that will be run by trac-all before an analysis. >> # It is >> used to set all parameters needed for the analysis. >> # >> # Remove a parameter >> from your dmrirc file if you want use the default value. >> # Parameters that >> don't have default values must be specified. >> # >> # Any other commands that >> you might want to run before an analysis can be added >> # to this file. >> # >> >> # Original Author: Anastasia Yendiki >> # CVS Revision Info: >> # $Author: >> ayendiki $ >> # $Date: 2013/02/16 22:49:06 $ >> # $Revision: 1.3.2.4 $ >> >> # >> # Copyright © 2011 The General Hospital Corporation (Boston, MA) "MGH" >> >> # >> # Terms and conditions for use, reproduction, distribution and >> contribution >> # are found in the 'FreeSurfer Software License Agreement' >> contained >> # in the file 'LICENSE' found in the FreeSurfer distribution, and >> here: >> # >> # >> https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense >> # >> # >> Reporting: freesurfer(a)nmr.mgh.harvard.edu >> # >> # >> >> # FreeSurfer >> SUBJECTS_DIR >> # T1 images and FreeSurfer segmentations are expected to be >> found here >> # >> setenv SUBJECTS_DIR >> >> /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/Analysis/C01_freesurfer/> >> >> # Output directory where trac-all results will be saved >> # Default: Same as >> SUBJECTS_DIR >> # >> >> # Subject IDs >> # >> set subjlist = (C01) >> >> # In case >> you want to analyze only Huey and Louie >> # Default: Run analysis on all >> subjects >> # >> >> # Input diffusion DICOMs (file names relative to dcmroot) >> >> # If original DICOMs don't exist, these can be in other image format >> # but >> then bvecfile, bvalfile, and nb0 must be specified (see below) >> # >> set >> dcmroot = >> >> /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/DICOMS/raw_dti/HURLE_LISA >> >> set dcmlist = (IM-0001-0001.dcm) >> >> # Diffusion gradient table >> # Must be >> specified if inputs are not MGH DICOMs >> # Three-column format, one row for >> each volume in the diffusion data set >> # Default: Read from DICOM header >> >> # >> # set bvecfile = >> /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvecs.txt >> >> # Diffusion >> b-value table >> # Must be specified if inputs are not MGH DICOMs >> # >> Single-column format, one value for each volume in the diffusion data set> # >> Default: Read from DICOM header >> # >> # set bvalfile = >> /bilhome/nyassi/Imaging_Data/ANSWER-Recovery/C01/bvals.txt >> >> # Number of >> low-b images >> # Must be specified if inputs are not DICOM >> # Default: Read >> from DICOM header >> # >> set nb0 = 0 >> >> # Perform registration-based >> B0-inhomogeneity compensation? >> # Default: 0 (no) >> # >> # set dob0 = 1 >> >> # >> Input B0 field map magnitude DICOMs (file names relative to dcmroot) >> # Only >> used if dob0 = 1 >> # Default: None >> # >> # set b0mlist = (huey/fmag/XXX-1.dcm >> dewey/fmag/XXX-1.dcm louie/fmag/XXX-1.dcm) >> >> # Input B0 field map phase >> DICOMs (file names relative to dcmroot) >> # Only used if dob0 = 1 >> # Default: >> None >> # >> # set b0plist = (huey/fphas/XXX-1.dcm dewey/fphas/XXX-1.dcm >> louie/fphas/XXX-1.dcm) >> >> # Echo spacing for field mapping sequence (from >> sequence printout) >> # Only used if dob0 = 1 >> # Default: None >> # >> # set >> echospacing = 0.7 >> >> # Perform registration-based eddy-current >> compensation? >> # Default: 1 (yes) >> # >> set doeddy = 1 >> >> # Rotate >> diffusion gradient vectors to match eddy-current compensation? >> # Only used >> if doeddy = 1 >> # Default: 1 (yes) >> # >> set dorotbvecs = 1 >> >> # Fractional >> intensity threshold for BET mask extraction from low-b images >> # This mask is >> used only if usemaskanat = 0 >> # Default: 0.3 >> # >> set thrbet = 0.3 >> >> # >> Perform diffusion-to-T1 registration by flirt? >> # Default: 0 (no) >> # >> set >> doregflt = 0 >> >> # Perform diffusion-to-T1 registration by bbregister? >> # >> Default: 1 (yes) >> # >> set doregbbr = 1 >> >> # Perform registration of T1 to >> MNI template? >> # Default: 1 (yes) >> # >> set doregmni = 1 >> >> # MNI >> template >> # Only used if doregmni = 1 >> # Default: >> $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz >> # >> # set mnitemp = >> /path/to/mni_template.nii.gz >> >> # Perform registration of T1 to CVS >> template? >> # Default: 0 (no) >> # >> set doregcvs = 0 >> >> # CVS template >> subject ID >> # Only used if doregcvs = 1 >> # Default: cvs_avg35 >> # >> # set >> cvstemp = donald >> >> # Parent directory of the CVS template subject >> # Only >> used if doregcvs = 1 >> # Default: $FREESURFER_HOME/subjects >> # >> # set >> cvstempdir = /path/to/cvs/atlases/of/ducks >> >> # Use brain mask extracted >> from T1 image instead of low-b diffusion image? >> # Has no effect if there is >> no T1 data >> # Default: 1 (yes) >> # >> set usemaskanat = 1 >> >> # Paths to >> reconstruct >> # Default: All paths in the atlas >> # >> # set pathlist = ( >> lh.cst_AS rh.cst_AS \ >> lh.unc_AS rh.unc_AS \ >> >> lh.ilf_AS rh.ilf_AS \ >> fmajor_PP fminor_PP >> \ >> lh.atr_PP rh.atr_PP \ >> lh.ccg_PP >> rh.ccg_PP \ >> lh.cab_PP rh.cab_PP \ >> >> lh.slfp_PP rh.slfp_PP \ >> lh.slft_PP >> rh.slft_PP ) >> >> # Number of path control points >> # It can be a single >> number for all paths or a different number for each of the >> # paths specified >> in pathlist >> # Default: 7 for the forceps major, 6 for the corticospinal >> tract, >> # 4 for the angular bundle, and 5 for all other paths >> # >> >> # set ncpts = (6 6 5 5 5 5 7 5 5 5 5 5 4 4 5 5 5 5) >> >> # List of training >> subjects >> # This text file lists the locations of training subject >> directories >> # Default: $FREESURFER_HOME/trctrain/trainlist.txt >> # >> # set >> trainfile = $FREESURFER_HOME/trctrain/trainlist.txt >> >> # Number of "sticks" >> (anisotropic diffusion compartments) in the bedpostx >> # ball-and-stick >> model >> # Default: 2 >> # >> set nstick = 2 >> >> # Number of MCMC burn-in >> iterations >> # (Path samples drawn initially by MCMC algorithm and >> discarded) >> # Default: 200 >> # >> # set nburnin = 200 >> >> # Number of MCMC >> iterations >> # (Path samples drawn by MCMC algorithm and used to estimate path >> distribution) >> # Default: 5000 >> # >> # set nsample = 7500 >> >> # Frequency >> with which MCMC path samples are retained for path distribution >> # Default: 5 >> (keep every 5th sample) >> # >> # set nkeep = 5 >> >> # Reinitialize path >> reconstruction? >> # This is an option of last resort, to be used only if one >> of the reconstructed >> # pathway distributions looks like a single curve. This >> is a sign that the >> # initial guess for the pathway was problematic, perhaps >> due to poor alignment >> # between the individual and the atlas. Setting the >> reinit parameter to 1 and >> # rerunning "trac-all -prior" and "trac-all >> -path", only for the specific >> # subjects and pathways that had this problem, >> will attempt to reconstruct them >> # with a different initial guess. >> # >> Default: 0 (do not reinitialize) >> # >> # set reinit = 0 >> >> >> >> > > > The >> information in this e-mail is intended only for the person to whom it >> is > addressed. If you believe this e-mail was sent to you in error and the >> e-mail > contains patient information, please contact the Partners Compliance >> HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to >> you in error > but does not contain patient information, please contact the >> sender and properly > dispose of the e-mail. > > >

1 0

Multiple skull strip problems--too much skull left AND cerebellum removed
by Hayley Dorfman 29 Mar '13

29 Mar '13

Hi everyone, With Bruce's extraordinary help, I've been able to get a formerly impossible subject through recon-all without error. However, the only remaining issue is that the skull strip is very strange, and is leaving too much skull at the top while simultaneously cutting off the entire cerebellum. As a result, it is also having some trouble segmenting, so I'd prefer to fix the skull strip in a way that will hopefully also fix the segmentation (see attached screenshots). I don't have any experience editing a bad skull strip that needs to have both brain added back in, and skull removed, so I'm not sure of the best order of operations. Does anyone have any suggestions? Would the best option be to use gcut for the skull and then go back in and clone the cerebellum afterwards? Thanks! Hayley

1 0

Download problem wih freesurfer-Darwin-lion-stable-pub-v5.2.0.dmg
by Leila Reddy 29 Mar '13

29 Mar '13

Hi, I'm trying to install the latest Mac OSX 64bit FreeSurfer version but when I click on the download link I get an error: 550 Failed to change directory. I can't find a file with this filename in ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/ either. Is this version not yet available (and when will it be available)? Thanks, Leila

2 1

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