Freesurfer December 2012

freesurfer@nmr.mgh.harvard.edu

101 participants
161 discussions

Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 06 Dec '12

06 Dec '12

The problem is that you have a version 4 analysis that you are trying to view with version 5 tools. To use version 5 visualization, you'll need to remake the analysis in version 5 and then reanalyze. Otherwise, you'll have to use the version 4 stream (instructions attached). It is somewhat difficult for me to support the version 4 stream because it is so old. doug On 12/06/2012 03:27 PM, Julia Foecker wrote: > I have the two versions 4 and 5 , but I am receiving the same error > messages with 5.1 > For example when I type in preproc-see there is no -surface as well. > Isn't there any other possibility to solve that issue? > > It may have also sth. to do with the computer. I have a new Mac, not > sure if this may be the reason. > As I said, I do not think this is due to the version...I just tried > that and similar requirements are missing when I am doing that with 5.1 > > Thanks again for further advices, > Julia > > > > On 12/6/12 11:56 AM, Douglas N Greve wrote: >> Julia, what version of FS are you using? It looks like pre-5.0. Can >> you upgrade to 5.1? There were a lot of changes in going from 4 to 5, >> and it is becoming increasingly hard to support version 4. >> >> doug >> >> >> >> On 12/06/2012 02:45 AM, Julia Foecker wrote: >>> thanks. >>> attached the info file. >>> >>> When I run the surf-sess command after that, it shows the functional >>> on a >>> surface (see attached but the values at the occip regions show >>> "inf." (see >>> figure 1 attached). >>> Moreover, when I try to load the occipital patch it shows me the >>> attached file >>> (fig.3) and I cannot use the command -> configure -> overlay to change >>> settings. >>> >>> I have used fake ecc. runs (I have recorded only polar runs). >>> >>> Would you have any further suggestions? >>> Thanks, >>> Julia >>> >>> On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve >>> <greve(a)nmr.mgh.harvard.edu> >>> wrote >>> >>>> It should automatically detect that this was a retinotopy analysis and >>>> then load the polar and eccen. Was this configured as a retinotopy >>>> analysis? Can you send me the >>>> >>>> $ANALYSIS_PHASE/analysis.info file? >>>> >>>> doug >>>> >>>> >>>> >>>> On 12/05/2012 04:12 PM, Julia Foecker wrote: >>>>> Hi Doug, >>>>> >>>>> I tried now several ways to get the maps on the surface: >>>>> >>>>> 1. When I am deleting -retinotopy flag and type in: >>>>> >>>>> >>>>>>> tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY >>>>>>> -analysis $ANALYSIS_PHASE >>>>> I got the message:no contrast has been specified >>>>> >>>>> (I do not have any contrasts in the analysis, just use polar angle >>>>> maps) >>>>> >>>>> >>>>> 2. I tried to use the commands on the website you referred to, but >>>>> I do not >>>>> have -surface in the preproc-sess (see attached) >>>>> The other commands depend on this preproc-sess command. >>>>> >>>>> >>>>> 3. I tried the following command >>>>> paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis >>>>> $ANALYSIS_PHASE >>>>> >>>>> >>>>> and I got the errors listed below... >>>>> >>>>> I am not sure how to procede. Would you have any further suggestions? >>>>> Many thanks, >>>>> Julia >>>>> >>>>> Thanks, >>>>> Julia >>>> >>>> >>>> >>>> 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. >>>> >> > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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how is fsnr computed?
by Alex Kell 06 Dec '12

06 Dec '12

freesurfers, i've been using my own scripts to compute tSNR for data i was running through FSL, but i'm now running the data through freesurfer and i wanted to better understand what the fsnr volumes spit out by selxavg3-sess are. i poked around the wiki and mailing archives and couldn't find answers to the following questions: 1. how is fsnr computed? tsnr is <mean_of_vox_time_course>/<std_of_vox_time_course> -- is fsnr the same thing with a different name? 2. what kind of preprocessing is done on the data before fsnr is computed? since freesurfer removes linear trends at the modeling stage, not the preprocessing stage, are linear trends removed from the data going into fsnr calculations? is anything else regressed out before fsnr is computed (e.g., other nuisance regressors)? 3. what's the difference between raw.fsnr.nii.gz, fsnr.nii.gz, and fsnr2.nii.gz? 4. is fsnr.dat the mean in the whole brain mask (i.e., gm and wm)? separately, random other question: what are the h.dat, h.nii.gz, and h-offset.nii.gz file/volumes? thanks in advance! alex kell

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image flip after use of mri_vol2surf/mri_surf2vol
by Fonteijn, H.M.J. (H.) 06 Dec '12

06 Dec '12

Hello, I'm relatively new to Freesurfer so chances are that this is a pretty basic error on my side but here goes anyhow. I'm trying to use mri_vol2surf for surface-based smoothing of functional MRI data. I would then like to extract time courses from the surface with spm functions by converting the surface to a volume again with mri_surf2vol. Specifically the commands I'm using are: bbregister --s subject0016 --mov volume0001.nii.gz --reg epi2T1.dat --init-spm --bold mri_vol2surf --mov volume0001.nii.gz --reg epi2T1.dat --surf-fwhm 8 --hemi lh --projdist-avg 0 1 0.1 --o ./volume0001Surf_lh.w --out_type paint mri_surf2vol --surfval volume0001Surf_lh.w paint --hemi lh --projfrac 0.5 --reg epi2T1.dat --o volume0001Surf2Vol_lh.nii --template volume0001.nii.gz Registration looks allright with tkregister2. I'm only using one volume (volume0001.nii.gz) to test this set of commands. However if I now view volume0001Surf2Vol_lh.nii in fslview, it shows the hemisphere on the right. I'm pretty sure that this is actually the left hemisphere but now flipped. I wonder how this can be solved. All the best, Hubert

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Running recon-all on a series of scans
by Natasha Jawa 06 Dec '12

06 Dec '12

Hi, Is it possible to run recon-all on a series of scans? I have multiple scans that I want to process longitudinally. The .nii files have all been converted to .mgz files and labelled sequentially (i.e., 001.mgz, 002.mgz, etc.) in /Applications/freesurfer/subjects/<subjid>/mri. I've tried running recon-all on this whole folder with the command line: recon-all -subjid <subjid> -all, but it does not execute properly. Do I have to run each of these scans separately using recon-all (i.e., do I need to use a separate terminal for each scan)? Thank you in advance for your time and help.

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Re: [Freesurfer] question retinotopic mapping
by Douglas N Greve 06 Dec '12

06 Dec '12

Julia, what version of FS are you using? It looks like pre-5.0. Can you upgrade to 5.1? There were a lot of changes in going from 4 to 5, and it is becoming increasingly hard to support version 4. doug On 12/06/2012 02:45 AM, Julia Foecker wrote: > thanks. > attached the info file. > > When I run the surf-sess command after that, it shows the functional on a > surface (see attached but the values at the occip regions show "inf." (see > figure 1 attached). > Moreover, when I try to load the occipital patch it shows me the attached file > (fig.3) and I cannot use the command -> configure -> overlay to change > settings. > > I have used fake ecc. runs (I have recorded only polar runs). > > Would you have any further suggestions? > Thanks, > Julia > > On Wed, 05 Dec 2012 17:03:31 -0500 Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > wrote > >> It should automatically detect that this was a retinotopy analysis and >> then load the polar and eccen. Was this configured as a retinotopy >> analysis? Can you send me the >> >> $ANALYSIS_PHASE/analysis.info file? >> >> doug >> >> >> >> On 12/05/2012 04:12 PM, Julia Foecker wrote: >>> Hi Doug, >>> >>> I tried now several ways to get the maps on the surface: >>> >>> 1. When I am deleting -retinotopy flag and type in: >>> >>> >>>>> tksurfer-sess -debug -s $SESSIONNAME -hemi lh -d $SESSIONDIRECTORY >>>>> -analysis $ANALYSIS_PHASE >>> I got the message:no contrast has been specified >>> >>> (I do not have any contrasts in the analysis, just use polar angle maps) >>> >>> >>> 2. I tried to use the commands on the website you referred to, but I do not >>> have -surface in the preproc-sess (see attached) >>> The other commands depend on this preproc-sess command. >>> >>> >>> 3. I tried the following command >>> paint-sess -s $SESSIONNAME -d $SESSIONDIRECTORY -analysis $ANALYSIS_PHASE >>> >>> >>> and I got the errors listed below... >>> >>> I am not sure how to procede. Would you have any further suggestions? >>> Many thanks, >>> Julia >>> >>> Thanks, >>> Julia >> >> >> >> 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. >> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Hippocampus volume
by Antonella Kis 06 Dec '12

06 Dec '12

Dear FS team, After I ran the recon-all to get the total cortical thickness, the volume of the left hypocampus ( = the number of voxels) equals to 2166 which I thought should be the total hippocampal volume. But if we add all the voxel numbers from the hippocampal subfield I will get a much larger number so I wonder which one represents the true total volume in terms of number of voxels. Can you also please advise how can I get differentiated hipocampus segmentation in form of head and body. Thank you. Antonella

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Re: [Freesurfer] Missing Insula and mri_label2vol
by José Ángel Pineda 06 Dec '12

06 Dec '12

Thanks Doug, now it works!! > for mac use > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol… > < > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol… > > > doug > > On 12/05/2012 05:11 AM, Jos? ?ngel Pineda wrote: > > Hi again, > > > > Sure I did set the permissions for execution, and also for this new > > one I am still having the same error. "/Exec format error. Binary file > > not executable/". I tried this on two macs (OSX Snow Leopard). I am > > still thinking that this is a compilation issue of the script, that is > > just compiled for linux. > > > > Thanks for your help > > > > Try this one > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol… > > > > On 12/04/2012 12:13 PM, Sarosh, Cyrus wrote: > > > Doug, > > > > > > I am unsure if Jose did this in his attempts to get it to work, > > but I ran this command after downloading and receiving this error > > initially and even after running this command I still receive the > > same error in the Windows virtual machine version of FreeSurfer. > > Any other ideas? > > > > > > Thanks, > > > > > > Cyrus > > > > > > -----Original Message----- > > > From: freesurfer-bounces(a)nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] On Behalf Of > > Douglas N Greve > > > Sent: Tuesday, December 04, 2012 11:58 AM > > > To: freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Subject: Re: [Freesurfer] (no subject) > > > > > > Hi Jose, did you set the permissions to be executable? > > > chmod a+x mri_label2vol > > > doug > > > > > > > > > On 12/04/2012 11:34 AM, Sarosh, Cyrus wrote: > > >> Doug, > > >> > > >> I am also curious about this mri_label2vol upgrade. Will this > > work on > > >> the Windows virtual machine version of FreeSurfer? I downloaded > and > > >> placed it in the FREESURFER/bin directory, but when trying to > > run it I > > >> receive an error that states: Exec format error. Binary file not > > >> executable. Thanks for your help. > > >> > > >> Cyrus > > >> > > >> *From:*freesurfer-bounces@nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> > > >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu > > <mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] *On Behalf Of *Jos? > > >> ?ngel Pineda > > >> *Sent:* Tuesday, December 04, 2012 9:07 AM > > >> *To:* freesurfer(a)nmr.mgh.harvard.edu > > <mailto:freesurfer@nmr.mgh.harvard.edu> > > >> *Subject:* [Freesurfer] (no subject) > > >> > > >> Thanks Doug, > > >> > > >> I already downloaded the new script for mri_label2vol, but it > > seems it > > >> is just compiled for linux, as I cannot execute it in my Mac. > > If it is > > >> so, could you please upload another compiled for mac, or source. > > >> Thanks > > >> > > >> Jose > > >> > > >> For the missing insula problem, try using a newer version of > > >> mri_label2vol > > >> > > >> > > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_labe > > >> l2vol > > >> > > >> The 2nd problem is not so easy to fix. You might be better > > off using > > >> aparc+aseg.mgz as input to mri_label2vol instead of the > > surface > > >> annotation. > > >> doug > > >> > > >> > > >> On 12/3/12 10:35 AM, Jos? ?ngel Pineda wrote: > > >> > Dear experts, > > >> > > > >> > I am registering cortical labels from Talairach > > coordinates to my > > >> > native T1. For doing this, I have run the next script > lines: > > >> > > > >> > > > >> > tkregister --targ brainmask.mgz --mov > > highres_brain.nii.gz --reg > > >> > T1FS2Highres.dat --regheader --noedit > > >> > > > >> > mri_label2vol --annot rh.aparc.annot --temp > > highres_brain.nii.gz > > >> --reg > > >> > T1FS2Highres.dat --o rh_aparc.nii.gz --hemi rh --subject > > FS --proj > > >> > frac 0 1 .1 --fillthresh .3 > > >> > > > >> > and the same for the left hemi. > > >> > > > >> > However I am finding two problems at the result. First > > Insula is > > >> > missing for both hemispheres, and second the cortical > > ROIs have the > > >> > shape of the figure attached, e.g. there are many voxels > > empty > > >> > > > >> > Im?genes integradas 1 > > >> > > > >> > I found in previous topics, that the mri_label2vol, was > > updated > > >> as it > > >> > left last volume from the list out of the conversion. I > > tried to > > >> > download it, but it is just compiled for linux, and > > since Im working > > >> > with mac I am not able to run it. Could you please give > > me any > > >> > comments to solve the problem with the missing voxels. > > >> > About the problem with the insula, the other option is > > to just > > >> extract > > >> > it with mri_annotation2label, but if I could get the > > mri_label2vol > > >> > working correctly it would be better. > > >> > > > >> > Thanks a lot > > >> > > > >> > Jose > >

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Re: [Freesurfer] Error upon trying to load NIFTI image in freeview
by Tudor Popescu 06 Dec '12

06 Dec '12

Thanks for your reply Yaniv! That is how I initially tried loading the NIFTI volumes (via the GUI, File|Load), but in the meantime I discovered what the problem was: there were spaces in the name of the folder containing the image, and apparently non-Windows OSs such as Xubuntu don't deal well with that! For future reference, as soon as you eliminate spaces - as well as possibly other'forbidden' characters from the file/folder name, FreeView will load the image with no problems. Tudor On 6 December 2012 00:44, Yaniv Kaufman <kaaniv.kaaufman(a)gmail.com> wrote: > Hi Tudor, > > I am not very experienced with Freeview, but did you try typing "freeview" > in the command line and using the File->Load Volume… from the GUI? > If that doesn't work maybe you can give me the exact command you used. > > Hope I could help. > Regards, > Yaniv > On 06/12/2012, at 1:47 AM, Tudor Popescu <tudor3(a)gmail.com> wrote: > > > Hi everyone, > > > > I tried opening a NIFTI (.nii.gz) image in freeview, but it gives me > repeated "Failed to load <image name>" errors. > > > > That same image loads fine in FSLview, but even when trying with other > NIFTI images, I get the same error. > > > > The default image > (/home/virtualuser/freesurfer/subjects/bert/mri/brainmask.mgz) opens fine > in freeview. > > > > I use FreeSurfer v5.1.0 on Xubuntu 9.10, running through VirtualBox on > WinXP. > > > > Many thanks for any help! > > Tudor > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)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. > >

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mris_ca_train / mris_ca_label problem
by Roan LaPlante 05 Dec '12

05 Dec '12

Hello freesurfer experts, I am having difficulties using mris_ca_train and mris_ca_label. I am trying to get third party-software to accept a user-defined parcellation in the form of a .gcs file, which I created from sample data using mris_ca_train. I have reproduced the portion of the workflow that is buggy. When I run the software, it calls mris_ca_train, followed by mris_ca_label and mri_annotation2label. On mri_annotation2label, it produces the following output and writes no label files: [truffles:mridat] (nmr-stable5.1-env) mri_annotation2label --subject nmr00535_FS --hemi lh --annotation icotest --outdir nmr00535_FS/label/regen subject = nmr00535_FS annotation = icotest hemi = lh outdir = nmr00535_FS/label/regen surface = white Reading surface /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/surf/lh.white Loading annotations from /autofs/cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/lh.icotest.annot reading colortable from annotation file... colortable with 643 entries read (originally /cluster/neuromind/rlaplant/mridat/nmr00535_FS/label/ico3_regenerated_clut_lh.txt) Seg base 0 *max index = -1* The annotation at this point is corrupted and cannot be opened in matlab and shows up empty in tksurfer. The annotation I started with as input to mris_ca_train shows up just fine. The commands i used for mris_ca_train and mris_ca_label are as follows: mris_ca_train -t $TEST_DIR/ico3_clut.txt lh sphere.reg ico3_morph $SUBJECTS $TEST_DIR/lh_test.gcs mris_ca_label nmr00535_FS lh sphere.reg $TEST_DIR/lh_test.gcs $TEST_DIR/nmr00535_FS/label/lh.icotest.annot Can anyone point out where my labels are being clobbered? thanks, R -- Roan LaPlante Athinoula A. Martinos Center for Biomedical Imaging

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aparc stats
by Donald Hagler 05 Dec '12

05 Dec '12

Is there a detailed description somewhere of how the gray matter volume values are calculated for the aparc stats files? Also, is the average thickness weighted by area?

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Freesurfer December 2012