Re: [Freesurfer] SMS3 pre-processing
oh, then I certainly would not worry about it. FC is really slow, so STC won't make much of a difference On 06/29/2015 07:01 PM, Rodriguez-Thompson, Anais wrote: > Hi Doug, > > Thanks for your reply. It's for our resting scan, so we don't have any > stimuli present. > > Best, > Anais > > Sent from my iPhone > >> On Jun 29, 2015, at 6:46 PM, Douglas N Greve >> wrote: >> >> I don't have a way to do SMS stc in 5.3 (it is there for 6.0). You might >> not need it for 1.15s TR. How long are your stimuli? >> >>> On 06/29/2015 04:41 PM, Rodriguez-Thompson, Anais wrote: >>> Hi all, >>> >>> We are currently using SMS3 scans for our resting state data. In order to >>> preprocess this scan, we are using the preproc-sess command which includes >>> slice-time correction. Since SMS3 is a multi-slice sequence that is >>> interleaved, do we need to use a different slice-time correction specific >>> to this type of sequence? If so, how do we specify the order of each set of >>> slices? Alternatively, since the TR is so short (1.15), would it be better >>> to skip the slice-time correction altogether using -nostc? >>> >>> Thanks for your help! >>> >>> Anais >>> ___ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 >> www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] SMS3 pre-processing
Hi Doug, Thanks for your reply. It's for our resting scan, so we don't have any stimuli present. Best, Anais Sent from my iPhone > On Jun 29, 2015, at 6:46 PM, Douglas N Greve > wrote: > > I don't have a way to do SMS stc in 5.3 (it is there for 6.0). You might > not need it for 1.15s TR. How long are your stimuli? > >> On 06/29/2015 04:41 PM, Rodriguez-Thompson, Anais wrote: >> Hi all, >> >> We are currently using SMS3 scans for our resting state data. In order to >> preprocess this scan, we are using the preproc-sess command which includes >> slice-time correction. Since SMS3 is a multi-slice sequence that is >> interleaved, do we need to use a different slice-time correction specific to >> this type of sequence? If so, how do we specify the order of each set of >> slices? Alternatively, since the TR is so short (1.15), would it be better >> to skip the slice-time correction altogether using -nostc? >> >> Thanks for your help! >> >> Anais >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] mni152reg
What version of mni152reg are you using? On 06/22/2015 05:17 AM, OKADA NAOHIRO wrote: > Hello Freesurfer Experts, > > I am trying to create a registration matrix from subject space to MNI152: > > mni152reg --s bert > > However, this error appeared: > > fslregister --mov > /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz --s bert --reg > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.dat > --dof 12 --tmp /usr/local/freesurfer/subjects/bert/tmp/mni152reg.4901 > --cleanup --lta > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.lta > ERROR: Flag --lta unrecognized. > --mov /usr/local/fsl/data/standard/MNI152_T1_2mm_brain.nii.gz --s bert > --reg > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.dat > --dof 12 --tmp /usr/local/freesurfer/subjects/bert/tmp/mni152reg.4901 > --cleanup --lta > /usr/local/freesurfer/subjects/bert/mri/transforms/reg.mni152.2mm.lta > > How can I make the mni152reg command work? > > Thanks in advance. > > Best, > Nao > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Extracting values from GLM Clusters
You can probably use the csdbase.y.ocn.dat file. Run mri_glmfit-sim --help to get more info On 06/19/2015 10:18 AM, Andrew Schoen wrote: > Hi, > > I have run some analyses using the GLM and cluster wise correction for > multiple comparisons outlined here: > http://freesurfer.net/fswiki/FsTutorial/GroupAnalysis > > For easy visualization of the groups, I was hoping to use the .annot > file created in the cluster wise correction step to extract values > for each subject and create scatter plots. However, as I understand > it, the .annot file created here exists only for fsaverage. Is there > a way to warp the .annot file to each subject (something > like mri_surf2surf), so as to run something like aparcstats2table > and extract the values? Or, is there a way to utilize the smoothed > concatenated file (from mris_preproc) to get at the same thing? > > Thanks! > > Andrew Schoen > University of Wisconsin - Madison > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Functional group analysis
I'm not sure what you mean. Why not use isxconcat-sess? Is your data already on the surface in fsfast? On 06/19/2015 08:26 AM, Silas wrote: > Dear FreeSurfer team, > > I'm currently doing a functional group analysis using FreeSurfer by > following your tutorial: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel > - > in order to concatenate the subjects data into one file you suggest > using the command isxconcat-sess. My questions is; is it possible to > use the command mris_preproc as in the structural analysis in this > step? I simply want to project functional beta-values onto the > fsaverage surface and analyze if there is a statistical significant > difference between two groups (after correcting for multiple comparisons). > > Best, Silas > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] SMS3 pre-processing
I don't have a way to do SMS stc in 5.3 (it is there for 6.0). You might not need it for 1.15s TR. How long are your stimuli? On 06/29/2015 04:41 PM, Rodriguez-Thompson, Anais wrote: > Hi all, > > We are currently using SMS3 scans for our resting state data. In order to > preprocess this scan, we are using the preproc-sess command which includes > slice-time correction. Since SMS3 is a multi-slice sequence that is > interleaved, do we need to use a different slice-time correction specific to > this type of sequence? If so, how do we specify the order of each set of > slices? Alternatively, since the TR is so short (1.15), would it be better > to skip the slice-time correction altogether using -nostc? > > Thanks for your help! > > Anais > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Retinotopic mapping
Hi try starting out on this web page http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastIndividualRetinotopyAnalysis On 06/16/2015 02:04 PM, lucas hosse wrote: > > Hi FreeSurfer experts, > > I have to construct the retinotopic mapping of angle and eccentricity. > > I have created with FreeSurfer the brain surface from the anatomical > files. > Once I have the alignment of the functional to the anatomical volume > (and so the position of the voxels) and I have the informations about > angle and eccentricity of the voxels, is it possible to obtain the > retinotopic mapping (with the correspondent informations about angle > and eccentricity)? > > Thank in advance! > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Timecourses In freesurfer
you can do something like this mri_vol2surf --mov func.nii.gz --hemi lh --reg register.dat --projfrac 0.5 --o func.lh.mgh tksurfer subject lh inflated -t func.lh.mgh doug On 06/13/2015 03:27 AM, jonathan oron wrote: > Hi, > In tksurfer I would like to be able to see the timecourse (Percent > Signal Change) for a vertice or cluster of vertices > I try to load a timecourse using file -> open timecourse and I cant > find any file that will load > Thanks! > Jonathan > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] help on mris_preproc
Hi David, did you resolve this? doug On 06/12/2015 04:56 PM, David C. Zhu wrote: > > Hi Doug, > > Thanks. > > I can see that the “mris_preproc” command reads the header information > in “register.dat”. > > I set the “.” as the $SUBJECTS_DIR, and thus it seems that > “mris_preproc” cannot locate the path. Is there a way to fix this? > > David > > Here is the (part of) output: > > -- > > end > > while ( $#argv != 0 ) > > while ( 27 != 0 ) > > set flag = $argv[1] ; shift ; > > set flag = --iv > > shift > > switch ( $flag ) > > switch ( --iv ) > > case "--ivp": > > case --ivp: > > if ( $#argv < 2 ) goto arg2err ; > > if ( 26 < 2 ) goto arg2err > > set ivp = $argv[1] ; shift ; > > set ivp = S02520110927_Free/sum_all_norm_IRF_EA.nii > > shift > > if ( ! -e $ivp ) then > > if ( ! -e S02520110927_Free/sum_all_norm_IRF_EA.nii ) then > > set irp = $argv[1] ; shift ; > > set irp = S02520110927_Free/register.dat > > shift > > if ( ! -e "$irp" ) then > > if ( ! -e S02520110927_Free/register.dat ) then > > set ivplist = ( $ivplist $ivp ) ; > > set ivplist = ( S00720110927_Free/sum_all_norm_IRF_EA.nii > S01420110908_Free/sum_all_norm_IRF_EA.nii > S01520110811_Free/sum_all_norm_IRF_EA.nii > S02520110927_Free/sum_all_norm_IRF_EA.nii ) > > set irplist = ( $irplist $irp ) ; > > set irplist = ( S00720110927_Free/register.dat > S01420110908_Free/register.dat S01520110811_Free/register.dat > S02520110927_Free/register.dat ) > > set subj = `head -1 $irp` ; > > set subj = `head -1 $irp` > > head -1 S02520110927_Free/register.dat > > set subjlist = ( $subjlist $subj ) ; > > set subjlist = ( freesurfer freesurfer freesurfer freesurfer ) > > set srcvol = 1 ; > > set srcvol = 1 > > breaksw > > breaksw > > end > > end > > … > > … > > … > > if ( 0 == 0 && 1 == 0 && 0 == 0 ) then > if ( $srcsurf && $srcvol ) then > if ( 0 && 1 ) then > if ( $srcsurf && $#projfrac != 0 ) then > if ( 0 && 0 != 0 ) then > if ( $catmean && $catstd ) then > if ( 0 && 0 ) then > if ( $#meas && $#isplist ) then > if ( 0 && 0 ) then > if ( $MeasIn && $CacheIn ) then > if ( 0 && 0 ) then > if ( $#ivplist != 0 ) then > if ( 12 != 0 ) then > if ( $#ivplist != $#subjlist ) then > if ( 12 != 12 ) then > endif > endif > if ( $#isplist != 0 ) then > if ( 0 != 0 ) then > if ( $paireddiff && ! $DoXHemi ) then > if ( 0 && ! 0 ) then > > if ( ! -e $SUBJECTS_DIR ) then > if ( ! -e . ) then > > > if ( $DoXHemi ) then > if ( 0 ) then > > echo "nsubjects = $#subjlist" ; > echo nsubjects = 12 > nsubjects = 12 > @ nthsubj = 1 ; > @ nthsubj = 1 > foreach subj ( $subjlist ) > foreach subj ( freesurfer freesurfer freesurfer freesurfer freesurfer > freesurfer freesurfer freesurfer freesurfer freesurfer freesurfer > freesurfer ) > set subjpath = $SUBJECTS_DIR/$subj > set subjpath = ./freesurfer > if ( ! -e $subjpath ) then > if ( ! -e ./freesurfer ) then > echo "ERROR: cannot find $subjpath" > echo ERROR: cannot find ./freesurfer > ERROR: cannot find ./freesurfer > exit 1 ; > exit 1 > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Douglas > Greve > *Sent:* Friday, June 12, 2015 3:51 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] help on mris_preproc > > Can you run the 2nd command with --debug as the first option and send > the terminal output? > doug > > On 6/12/15 12:09 PM, David C. Zhu wrote: > > Dear FreeSurfer experts: > > I have been using FreeSurfer for segmentation and for volumetric > analyses. I want to give a try to use it for surface-based fMRI > analyses. > > I encountered some issues with mris_preproc to assemble IRF > results to the fsaverage surface. Please advise on how to resolve > these issues. > > Here is what I did: > > After finishing “recon-all” on each subject, I ran this following > on each subject. > > bbregister --mov reg_cat_TSall_before_blur.nii --bold --s > freesurfer --init-fsl --lta register.lta > > “reg_cat_TSall_before_blur.nii” is the EPI fMRI time series > assembled together. > > Then I calculated the IRF percent signal changes for different > conditions. “sum_all_norm_IRF_EA.nii” is for one condition. > > Now I want to assemble the “sum_all_norm_IRF_EA.nii” from each > subject and put them on the fsaverage surface. I got the following > errors: > > mris_preproc --hemi rh --o rh.fsaverage.sumEA.mgh \ > > --iv S00720110927_Free/sum_all_norm_IRF_EA.nii > S00720110927_Free/register.lta \ > > --iv S01420110908_Free/sum_all_norm_IRF_EA.nii > S01420110908_Free/register.lta \ > > --iv S01520110811_Free/sum_all_norm_IRF_EA.nii > S01520110811_Free/register.lta \ > > --iv S02520110927_Free/sum_all_norm_IRF_EA.nii > S02520110927_Free/register.lta \ > > --iv S02720111028_Free/sum_all_norm_IRF_EA.nii > S02720111028_Free/register.lta \ > > --iv S0282007_Free/sum_all_norm_IRF_EA.nii
Re: [Freesurfer] Import mask from FSL to FS for performing seed-based FS-FAST functional connectivity
Hi Stefano, sorry for the delay, I was traveling. It sounds like you just need to run fcseed-config and specify -seg ROI_MASK.mgz and -segid 1 (assuming your ROI_MASK is in $SUBJECTS_DIR/subject/mri). If the mask is in the orig.mgz space, then everything should work ok, but you can look at it with tkmedit -f orig.mgz -aux ROI_MASK.mgz You can also run mri_label2vol --seg $SUBJECTS_DIR/subject/mri/ROI_MASK.mgz --reg register.dof6.dat --temp template.nii.gz --fillthresh 0.5 --o func.ROI_MASK.nii where template.nii.gz and register.dof6.dat are in the functional run folder doug On 06/12/2015 04:39 PM, std...@virgilio.it wrote: > Hi list, > I working on the combination of MRS and FS-FAST analysis. > I have extracted the grey matter within voxel (I will call it > "ROI_MASK") by using FSL tools and now it is in the same space of > orig.mgz (the roi mask is perfectly overlapped on orig.nii.gz when I > use fslview). > > I'd like to import it to FS for performing seed-based FS-FAST > functional connectivity. > The seed should the ROI MASK (GM within voxel). > > I know that the FSL and FS operate in different space and orientation. > I think to have resolved the problem of different space by using > orig.nii.gz to create ROI mask by FSL. > However, I'm strongly worried for orientation issues. > I have read the guidelines in FSL and FS sites, but I'm quite confused. > In detail, I'd like to ask whether I should use "mri_cor2label" to > transform ROI mask created by FSL to label. > > Furthmore, I'd like to be sure of the position of the ROI. How can I > visualize it to be sure that the seed of my FS-FAST analysis is > effectively the my ROI_MASK? > > I hope in your help. > > Thanks in advanced. > > > Stefano > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] SMS3 pre-processing
Hi all, We are currently using SMS3 scans for our resting state data. In order to preprocess this scan, we are using the preproc-sess command which includes slice-time correction. Since SMS3 is a multi-slice sequence that is interleaved, do we need to use a different slice-time correction specific to this type of sequence? If so, how do we specify the order of each set of slices? Alternatively, since the TR is so short (1.15), would it be better to skip the slice-time correction altogether using -nostc? Thanks for your help! Anais ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] FW: FW: Functional group analysis
How have your processed the fMRI data? If you have beta maps in the native functional space, then you'll need to run bbregister on a template from the native space, then run mri_vol2surf, the mri_concat, then mri_glmfit doug On 6/28/15 1:17 PM, Silas wrote: Dear all, Can anyone help me with this question? Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Date: Wed, 24 Jun 2015 11:35:28 +0200 Subject: [Freesurfer] FW: Functional group analysis Dear FreeSurfer team, I'm working on a functional analysis using FreeSurfer. I've already preprocessed my fMRI data and now I would like to analyze this data using mri_glmfit. My input is the prepared beta estimates for the fmri data (regression coefficients) and two groups (with activated regions for different muscles in the hand; musculus abductor digiti minimi vs first dorsal interossei). I do not want to smooth my data. Which command/step do you suggest in order to implement this data into mri_glm? I've experimented with mris_preproc and the creation of a FSGD-file in the structural analysis in order to implement my data in the GLM. Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Functional group analysis Date: Fri, 19 Jun 2015 14:26:20 +0200 Dear FreeSurfer team, I'm currently doing a functional group analysis using FreeSurfer by following your tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel - in order to concatenate the subjects data into one file you suggest using the command isxconcat-sess. My questions is; is it possible to use the command mris_preproc as in the structural analysis in this step? I simply want to project functional beta-values onto the fsaverage surface and analyze if there is a statistical significant difference between two groups (after correcting for multiple comparisons). Best, Silas ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)
Hi Christopher mris_info --v will print out the surface RAS coords of the vertex (plus some other stuff that you probably don't care about) Bruce On Mon, 29 Jun 2015, Milde, Christopher wrote: Dear FS experts I extracted the vertex indices of several subjects. But unfortunately I did not extract the corresponding Vertex RAS values. Is there a command to translate the Vertex Index into a Vertex RAS so that I do not have to scroll through all the subjects again? I would like to script the translation from Vertex Index to Vertex RAS Best wishes, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Vertex Index to Vertex RAS withouth using surface visualizer (tksurfer or tkmedit)
Dear FS experts I extracted the vertex indices of several subjects. But unfortunately I did not extract the corresponding Vertex RAS values. Is there a command to translate the Vertex Index into a Vertex RAS so that I do not have to scroll through all the subjects again? I would like to script the translation from Vertex Index to Vertex RAS Best wishes, Christopher ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] too much white matter
Hi Clara are you sure you put the control points in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including the subcortical areas and lots of the cortical ribbon. See attached picture. Could you explain how this happens because the logfile says it ran without error. In these cases I've deleted the whole thing and preprocessed the scan from scratch. I was wondering if there's a better way to deal with this like going a step back if that's possible. Cheers, Clara Kühn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] finding local extrema in surface data
Not the fastest approach, but for each vertex, you could find the neighbors and then test if the vertex is the maximum. There are matlab functions for getting the list of neighboring vertices. Best Regards, Donald McLaren = D.G. McLaren, Ph.D. Research Fellow, Department of Neurology, Massachusetts General Hospital and Harvard Medical School Postdoctoral Research Fellow, GRECC, Bedford VA Website: http://www.martinos.org/~mclaren Office: (773) 406-2464 = This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (773) 406-2464 or email. On Tue, Jun 23, 2015 at 3:49 AM, Gronenschild Ed (NP) < ed.gronensch...@maastrichtuniversity.nl> wrote: > Hi Sabine, > > Perhaps you can transform ?h.sphere and corresponding surface data > into a polar image in which you can try to find the local extrema. > > Cheers, > Ed > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Recon-all error
Hi,I keep getting an error when I run recon-all and can’t figure out what is wrong. I would really appreciate your help. I’ve attached the log file.Thank you so much,Emad Emad Ahmadi, MD---Research FellowDepartment of RadiologyMassachusetts General HospitalHarvard Medical School25 New Chardon Street, Suite 400Boston, MA 02114Tel: 617 726 5237Email: e...@nmr.mgh.harvard.edu recon-all.log Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] Fwd: Recon-all different execution time for same subjects
Dear freesurfer experts, I'm performing a study about the variability of the execution time of recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for two identical MRIs (two copies of the same MRI), takes different execution time. I'm performing the execution using GPUs capability, but the same is happening for the CPU-only executions. Checking the output logs I found i.e CA Reg, the number of the iterations is different, what's the main source of this variability? I guess that maybe It is related to some random seeds used and the convergence of the implemented methods. CA Reg example: Execution Time 1 - Subject 1: 00:25:23 Execution Time 2 - Subject 1: 00:32:14 In both cases the computing node was used exclusively for the recon-all execution. Did you measured the percentage of this variability? Can we extract some measures to compare the work realized in each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] 2D sphere co-ordinates
Hi Jonathan sure. The sphere.reg acts as a lookup table for this. For the vertex you want, just compute it's spherical coordinates from the sphere.reg file and you should be all set. cheers Bruce On Mon, 29 Jun 2015, jonathan oron wrote: Hi Freesurfer Experts!I'm looking to find the 2D co-ordinates for a vertex in the fsaverage surface I can find their 3D volume co-ordinates using read_surf but I'd like the 2D coordinates. I'll explain: I would like to study properties of the inflated STS. For each of the vertices I can find the 3-D volume co-ordinates but I'd like a 2D co-ordiante or at least the theta and phi. In a rough analogy, I'd like to get STS coordinates per vertice in an XY fashion like I can get a map of the world in longtitude/latitude. Is this possible? Thanks! Jonathan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
[Freesurfer] 2D sphere co-ordinates
Hi Freesurfer Experts! I'm looking to find the 2D co-ordinates for a vertex in the fsaverage surface I can find their 3D volume co-ordinates using read_surf but I'd like the 2D coordinates. I'll explain: I would like to study properties of the inflated STS. For each of the vertices I can find the 3-D volume co-ordinates but I'd like a 2D co-ordiante or at least the theta and phi. In a rough analogy, I'd like to get STS coordinates per vertice in an XY fashion like I can get a map of the world in longtitude/latitude. Is this possible? Thanks! Jonathan ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
Re: [Freesurfer] Preproc-sess failed
Sorry, I didn't have access to my CentOS machine, the 32-bit libraries use the suffix i686 instead of i386, so try sudo yum remove libXp.i686 By removing the 32-bit version you essential ensure only the 64-bit version is available when the application tries to load libXp. Hope that works. My machine only has the 64-bit version installed. Although technically, it should not matter if you have both installed on the system as it should automatically pick the correction version. If it doesn't work, you could try to run find / -type f -iname "libXp.so*" -print to check if the libXp libraries might be installed somewhere else. It may take some time to scan the entire system and any mounted volumes. You can use the `file ` command to check if the library is 32 or 64-bit, and remove any 32-bit or even 64-bit version outside /usr/lib64 (BEWARE: removing libraries is at risk of breaking functioning of other application that depend on that particular library. If necessary, you can always run `sudo yum install libXp.i686` to install the 32-bit version again) On Jun 29, 2015, at 08:10 AM, Thục Trinh wrote: Hi, "yum remove libXp.i386" command returns with No Packages marked for removal This is my output for:'file $FREESURFER_HOME/bin/3dvolreg.afni' /usr/local/freesurfer/bin/3dvolreg.afni: ELF 64-bit LSB executable, x86-64, version 1 (GNU/Linux), statically linked, stripped 2015-06-26 16:19 GMT+07:00 Jalmar Teeuw : Have you tried removing the 32-bit version of the libraries? I believe it is yum remove libXp.i386 What is the output of file $FREESURFER_HOME/bin/3dvolreg.afni Maybe you could try locate all the libXp.so on your system and see if there is a local 32-bit copy find / -type f -iname "libXp.so*" On 25 Jun 2015, at 09:45, Thục Trinh wrote: the lib files are now in /usr/lib64, the ERROR still the same after I set a new path for shared lib with this command in .bashrc file export LD_LIBRARY_PATH=/usr/lib64:$LD_LIBRARY_PATH the Error still the same. 3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32 output of uname -a on my system is: Linux localhost.localdomain 2.6.32-358.el6.x86_64 #1 SMP Fri Feb 22 00:31:26 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux 2015-06-25 14:15 GMT+07:00 Jalmar Teeuw : Is still gives you the same error? I'm not certain about libXpm; I recall having to install certain libraries on a slimmed down version of Centos 6.5, libXp and libXpm were amongst those libraries. For me, the lib files are stored in /usr/lib64 Try find /usr/lib64 -type f -iname "libXp*" -print This will search for the files. What is the output uname -a On your system? On 25 Jun 2015, at 09:01, Thục Trinh wrote: Hi, After complete install the suitable version of shared library as you suggested, I cannot find any file name libXpm.x86_64 to set the new path for shared library. Ps: Is there any differences between libXpm.x86_64 and libXp.x86_64 2015-06-24 16:03 GMT+07:00 Jalmar Teeuw : That sounds more like you have only the 32-bit version of the libXp installed when 64-bit is required. Are you using the 64-bit version of Freesurfer 5.3.0 for CentOS 6 that is available on the downloads page? Have you tried sudo yum install libXp.x86_64 on the terminal? This should install the 64-bit libraries alongside the 32-bit libraries of libXp. If I recall correctly, you might also need the libXpm libraries, use sudo yum install libXpm.x86_64 On 24 Jun 2015, at 04:49, Thục Trinh wrote: I did that, and run the command 3dvolreg.afni on Terminal to check. The Error still remain: 3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32 2015-06-23 10:39 GMT+07:00 Z K : From reading the email thread history, it appears you may have downloaded the apple OS X version of 3rvolreg.afni and overwrote the original, which is the cause of the error. Please extract the original version of that binary from the original tarball. If you no longer have it you can download it from this page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke On Jun 22, 2015, at 11:29 PM, Thục Trinh wrote: hello, I am using CentOS release 6.4 ( final) 64bit and Freesurfer v.5.3.0. I think that makes the confliction. 2015-06-23 8:26 GMT+07:00 Thục Trinh : Hello Douglas and ZK, I set the path for shared library in my .basrch file, but it still does not work and comes up with this Error: 3dvolreg.afni: error while loading shared libraries: libXp.so.6: wrong ELF class: ELFCLASS32 ERROR: 3dvolreg.afni Invalid null command. Trinh 2015-06-23 3:03 GMT+07:00 Z K : Trinh, Attempt to determine where libXp.so.6 was installed on your system after you installed it using yum. For example, on my system libXp.so.6 exists in directory "/usr/lib64". Once you determine the location where the library resides, add that directory to your LD_LIBRARY_PATH after you source freesurfer. $> source $FREESURFER_HOME/SetUp
Re: [Freesurfer] FW: FW: Functional group analysis
Hi Bruce, I will. Thanks! Best, Silas Date: Sun, 28 Jun 2015 13:20:30 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: FW: Functional group analysis Hi Silas Doug (who normally answers this kind of question) is on vacation. Can you repost in a few days? cheers Bruce On Sun, 28 Jun 2015, Silas wrote: > Dear all, > Can anyone help me with this question? > > Best, Silas > > > From: silasniel...@hotmail.com > To: freesurfer@nmr.mgh.harvard.edu > Date: Wed, 24 Jun 2015 11:35:28 +0200 > Subject: [Freesurfer] FW: Functional group analysis > > Dear FreeSurfer team, > I'm working on a functional analysis using FreeSurfer. I've already > preprocessed my fMRI data and now I would like to analyze this data using > mri_glmfit. My input is the prepared beta estimates for the fmri data > (regression coefficients) and two groups (with activated regions for > different muscles in the hand; musculus abductor digiti minimi vs first > dorsal interossei). I do not want to smooth my data. > > Which command/step do you suggest in order to implement this data into > mri_glm? > > I've experimented with mris_preproc and the creation of a FSGD-file in the > structural analysis in order to implement my data in the GLM. > > Best, Silas > > > From: silasniel...@hotmail.com > To: freesurfer@nmr.mgh.harvard.edu > Subject: Functional group analysis > Date: Fri, 19 Jun 2015 14:26:20 +0200 > > Dear FreeSurfer team, > I'm currently doing a functional group analysis using FreeSurfer by > following yourtutorial: > https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFa > stGroupLevel - in order to concatenate the subjects data into one file you > suggest using the command isxconcat-sess. My questions is; is it possible to > use the command mris_preproc as in the structural analysis in this step? I > simply want to project functional beta-values onto the fsaverage surface and > analyze if there is a statistical significant difference between two groups > (after correcting for multiple comparisons). > > Best, Silas > > ___ Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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.
