Freesurfer November 2013

freesurfer@nmr.mgh.harvard.edu

120 participants
198 discussions

Re: [Freesurfer] Error when using --mask flag in mri_glmfit
by Douglas N Greve 21 Nov '13

21 Nov '13

The label will be totally off because it was not created in the conformed anatomical space of fsaverage. Does the mask look ok? If you want to view the label, use something like tkmedit -f $SUBJECTS_DIR/fsaverage/mri.2mm/orig.mgz -ov sig.mgh -seg $SUBJECTS_DIR/fsaverage/mri.2mm/aseg.mgz doug On 11/19/2013 08:41 AM, Suzanne Oosterwijk wrote: > Hi Doug, > > I use the following command to open tkmedit and then I load the mask, > the ocn.mgh file or the original label (created by mri_binarize) as a > segmentation (through the tkmedit menu). In this case a label does > open, but it is totally off. > > tkmedit fsaverage orig.mgz -aux brain.mgz -bc-main-fsavg -overlay > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol/omnibus/glm.amygdala/osgm/sig.mgh > -fthresh 2.3 -fmax 4 -aparc+aseg > > Thanks! > Suzanne > > > > > > > > > On Thu, Nov 14, 2013 at 8:48 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: > > What is your tkmedit command used to view the segmentation? > doug > > > On 11/14/2013 07:10 AM, Suzanne Oosterwijk wrote: > > Hi Doug, > > Thanks for the code, this works. Nevertheless, I am a bit > unsure about whether the masks that are used as input into > this command are correct. I like to check all the stages of > the process and when I open the mask.mgh file within the > appropriate glm folder, the segmentation is totally off (the > putamen is somewhere in the OFC). Furthermore, even though the > file that holds the output cluster from the Monte Carlo > simulation (mc-z.pos.23.lh.sig.cluster.mgh) seems correct, the > segmentation file that I use as input into the mri_segstats > command is also totally off (mc-z.pos.23.lh.sig.ocn.mgh) when > I load it in tkmedit. Am I loading it incorrectly as a > segmentation? Does this have anything to do with the fact that > you advised me to use the 2mm version > fsaverage/mri.2mm/aseg.mgz? Should I adapt for that in my > tkmedit command? > > Finally, I also run into a problem with the nucleus accumbens > specifically. For some reason I get an error when I run the > glmfit and mc simulation within this specific mask. First I > make the mask: > > mri_binarize --match 26 --i > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri.2mm/aseg.mgz > --o > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/accumb_lh.mgz > > Then I run glmfit: > > set labels = (accumb) > foreach label ($labels) > mri_glmfit --y ces.nii.gz --osgm --glmdir glm.${label} --mask > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/${label}_lh.mgz > mri_glmfit-sim --glmdir glm.${label} --sim mc-z 10000 2.3 > mc-z.pos.23.lh --sim-sign pos > end > > But I get an error saying: > > FWHM = -nan > ERROR: input FWHM is NaN (not a number). > Check the mask in the glm directory. > > Any ideas what I am doing wrong? > > Thanks again! > > Suzanne > > > On Tue, Nov 5, 2013 at 12:04 AM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> wrote: > > > Hi Suzanne, there is probably an easier way to do this. If you > create contrasts of each condition vs baseline then run > isxconcat-sess on each, you can then run something like > > mri_segstats --seg mc-z.pos.23.lh.sig.ocn.mgh --i > condition1.nii.gz --avgwf condition1.table.dat --excludeid 0 > > where condition1.nii.gz is the output of isxconcat-sess for > condition 1. The output fo mri_segstats will be > condition1.table.dat which will have a row for each > subject and a > column for each of the clusters > > doug > > > > On 11/01/2013 09:51 AM, Suzanne Oosterwijk wrote: > > > Hello again, > > I am stuck again in my analysis and I am not sure that > my code > is right. I want to do the following. With a Monte Carlo > simulation I search for significant clusters within a > particular ROI in my all conditions vs baseline > contrast. Then > I want to translate this functional cluster to each > individuals native space (as a label) and extract percent > signal change for each condition separately from that > label. > This is no problem in my surface analysis, but I am > not sure > how to do this in the volume. I ran the Monte Carlo > simulation > within the mask, which provides a segmentation called > mc-z.pos.23.lh.sig.ocn.mgh. I assume that this would > be the > label that would go into mri_vol2vol to translate the > cluster > to native space. I found on the website, however, that you > need to use tkregister first. So I used the following > code, > but I am doubtful about whether I am doing this right. > > tkregister2 --mov > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol > /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh --s > ff_01_030512 --regheader --reg > ff_01_030512/register.dat --surf > > The results of this command do not look good at > all....(see > attached image). The cluster in the -mov file does not > overlap > with the amygdala. For the next step, I assumed to use > mri_vol2vol to save the cluster as a native space label, > although I'd like to make sure the first step is correct > before continuing with this step. > > mri_vol2vol --mov > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_functional/ff_image/feedback_gamma_image_vol > > /omnibus/glm.amygdala/osgm/mc-z.pos.23.lh.sig.ocn.mgh > --reg > ff_01_030512/register.dat --fstarg --interp nearest --o > ff_01_030512/label/lh.amygdala.imact.mgz --s ff_01_030512 > > > What am I missing? Is the translation off because I did > something wrong, or does that point to a deeper issue? > > > Any help is much appreciated! > > > Suzanne > > > > On Tue, Oct 29, 2013 at 6:04 PM, Douglas N Greve > <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: > > Hi suzanne, you'll need to use the 2mm version > fsaverage/mri.2mm/aseg.mgz > doug > > On 10/29/2013 11:46 AM, Suzanne Oosterwijk wrote: > > Hello all, > > > > I want to run a Monte Carlo simulation within a > volume > ROI and I am > > running into a problem when I use the --mask > flag while > running > > glmfit. My question is very similar to the > question asked in > > "[Freesurfer] Volume-based Monte Carlo > Restricted to a > within mask > > area" but I could not find the response to this > question. > > > > Here is my code. > > > > First, I created a volume mask with mri_binarize: > > > > mri_binarize --match 18 --i > > > > home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/fsaverage/mri/aseg.mgz > > --o > > > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > > > I checked the mask and it looked good. Then I > use the > mask in > glmfit. > > > > mri_glmfit --y ces.nii.gz --osgm --glmdir > glm.amygdala_lh --mask > > > > /home/sooster1/Desktop/FALSE_FEEDBACK_imaging/DATA/feedback_structural/ROI_handmade_labels/amygdala_lh.mgz > > > > When I do this, I get the following error: > > > > ERROR: dimension mismatch 1 between y and mask > > > > I guess this means that the ces.nii.gz file and mask > file don't > match, > > but I have no idea how to solve this. Any thoughts? > > > > Thanks! > > Suzanne > > > > > > -- > > > > Suzanne Oosterwijk, Ph.D. > > > > Postdoctoral Researcher > > > > Department of Social Psychology > > > > University of Amsterdam > > > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>>>va.nl <http://va.nl> > <http://va.nl> > <http://va.nl> <http://va.nl> > > > > > https://sites.google.com/site/suzanneoosterwijk/ > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>>> > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 > <tel:617-724-2358>>> > Fax: 617-726-7422 <tel:617-726-7422> > <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 > <tel:617-726-7422> > > <tel:617-726-7422 <tel:617-726-7422>>> > > Bugs: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu>> > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > <mailto:Freesurfer@nmr.mgh.harvard.edu > <mailto: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. > > > > > -- > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu> > <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>>va.nl <http://va.nl> > <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > -- Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Phone Number: 617-724-2358 <tel:617-724-2358> > <tel:617-724-2358 <tel:617-724-2358>> > Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 > <tel:617-726-7422>> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu > <mailto:s.oosterwijk@neu.edu>>va.nl <http://va.nl> <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 <tel:617-724-2358> > Fax: 617-726-7422 <tel:617-726-7422> > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > > > > -- > > Suzanne Oosterwijk, Ph.D. > > Postdoctoral Researcher > > Department of Social Psychology > > University of Amsterdam > > s.oosterwijk@u <mailto:s.oosterwijk@neu.edu>va.nl <http://va.nl> > > https://sites.google.com/site/suzanneoosterwijk/ > -- 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: 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/

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Re global lgi values
by Anna Jonsson 21 Nov '13

21 Nov '13

Dear list, I have a question about extracting global lgi values/hemisphere. I think I have managed to do it correctly using : mri_segstats --slabel subj lh $SUBJECTS_DIR/subj/label/lh.cortex --i $SUBJECTS_DIR/subj/surf/lh.pial_lgi --sum lh.aparc.pial_lgi.stats (Please let me know if this is not correct) I then get this output ( for each individual) ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 7953 5220.0 Seg0000 2.4055 0.4052 1.5796 2.9763 1.3967 2 1 156737 101379.9 Seg0001 2.9472 0.9038 1.7030 6.0007 4.2977 I assume one of these values (if above command has worked correctly) contains the mean lgi value for the left hemisphere. Can somebody please tell me which of the above values is the correct lgi value? Additionally, what units are lgi measured in, and are values between 1-5 what is considered normal? Thank you very much Anna

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aparc.DKTatlas40
by krista kelly 21 Nov '13

21 Nov '13

I'm using freesurfer v. 5.3 and I see a new annotation, aparc.DKTatlas40.annot in the labels folder. Can anyone tell me what the difference between this and the apart.annot is? Does it just have 40 labels versus the 36 found in the older version? Thanks!

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recon-all -s subjects -all unexpected termination
by Rujing Zha 21 Nov '13

21 Nov '13

Dear all, I have run recon-all for some subjects,but this code is unexpected terminated before it normally end. Can I run the code agian directly without deleting some outputs obtained from recon-all? That is to say, part of recon-all outputs do exist(as I have run recon-all previously), then recon-all new output will overwrite the existing files when I run recon-all again? All the best. 2013-11-21 Rujing Zha

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Re: [Freesurfer] trac-all inquiry
by Anastasia Yendiki 21 Nov '13

21 Nov '13

Hi David - This log only shows output from the -path step and not from the -prep step. The file that's missing should be created during the -prep step, so there's no way to figure out what went wrong without seeing the output from the pre-processing. Please cc the freesurfer list on your reply. Thank you, a.y On Sat, 16 Nov 2013, David Soto wrote: > Thanks, please see attachedI only noticed this > ERROR: Could not open/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_avg33_m > ni_bbr_cpts_5_std.txt > cheers > DS > > > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi David - Can you please send us the trac-all.log file for this > subject? > Without seeing where it stopped and what error messages there > are it's > hard to guess what's going on. > > Thanks, > a.y > > On Fri, 15 Nov 2013, David Soto wrote: > > > Hi - > > trac-all completed in all my Ps except one > > and I noticed that the dlabel/diff output does not contain > all the files > > > > I assessed whether it could be do to poor registration, by > checking > > the aparc+aseg > > file and looks allright > > > > I also checked the registration of FA maps to standard space > by > > freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > > dtifit_FA.bbr.nii.gz > > and seems fine > > > > also > > > > freeview -v brain_anat_orig.nii.gz lowb_brain.nii.gz > > > > which also seems fine > > > > any ideas pls? > > > > thanks! > > > > ds > > > > > > > > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > I suspect the current problem is caused by poor > registration. > > Have you checked the aparc+aseg and/or the registration > from > > diffusion to anatomical and from anatomical to MNI? > > > > On Fri, 16 Aug 2013, David Soto wrote: > > > > > > > > -- > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > > > 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. > > > > > -- > http://www1.imperial.ac.uk/medicine/people/d.soto/ > >

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Bedpost Not successfully completed
by ebelleau＠uwm.edu 20 Nov '13

20 Nov '13

Hello, I am finding that my bedposting is not completing successfully. I was able to get my first two subjects to run successfully, however, for the other two subjects that I have run I have gotten the following message: For some reason the bedpostX process DOES NOT appear to have successfully completed. Please examine your results carefully. /opt/psych_imaging/Freesurfer_5.3//bin/bedpostx_mgh: line 345: kill: (30896) - No such process Any ideas of what I should be looking for or troubleshooting to get this step to work? Thanks so much, Emily

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accessing old releases?
by Ruth Carper 20 Nov '13

20 Nov '13

Hi, I need to reinstall an older version of Freesurfer, but the only link I found: Old releases are here. seems to require a login and password. How can I access this?

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hippocampus region in an atlas?
by Gregg, Brian E. 20 Nov '13

20 Nov '13

Hello, I didn't see hippocampus listed in the Desikan-Killiany, Destrieux, or DKTatlas40 atlases. Is there an existing atlas that contains the hippocampal subfields? If not, what options exist for getting the hippocampus into an atlas? Thank you, Brian

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T2pial/FLAIRpial processing issues
by Martijn Steenwijk 20 Nov '13

20 Nov '13

Dear all, There seem to be some serious issues with the T2pial / FLAIRpial processing options provided in the latest versions of FreeSurfer. First of all, although not clearly documented, T2pial / FLAIRpial processing does require the FSLDIR to be set (in order to use bbregister with --init-fsl). If not set, recon-all will finish just without using the T2 or FLAIR information. Importantly, no clear warning about this is given although the user expects that T2/FLAIR has been used for pial surface refinement. I think this is a very easy source of errors, so it might be a good idea to just throw an error when FSLDIR is missing and T2pial/FLAIRpial processing is requested. Second, if FSLDIR has been set. T2pial/FLAIRpial uses bbregister with FLIRT initialisation to align the T2 or FLAIR image to orig.mgz. However, we have some high-res 3DFLAIR data in which this registration (more specifially, the FLIRT initialisation step of bbregister) seems to fail in more than half of the cases. Apparently, the FSL initialisation is not capable to change the orientation such that it fits to the coordinate system used for orig.mgz. Again, no warning or error is thrown, but the processing just continues with the wrong registration and without noticing the results will get worse compared to not using T2 or FLAIR. Although I know its essential to look at the output data; would it be possible to put some effort in letting the user know that things got wrong? As a sidenote; I tried to fix this registration issue, but it seems to be very complicated using bbregister (other than just inserting my own registration obtained by using FLIRT to register native FLAIR to native T1, and subsequently transform the result to Freesurfer space in order to obtain FLAIR.mgz). Best, Martijn

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(no subject)
by pietro de rossi 20 Nov '13

20 Nov '13

Good morning Dr Vinke, did you have the chance to take a look at the subject I uploaded a few days ago? thanks again. Kind regards, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Laboratorio di Neuropsichiatria, Dipartimento di Neurologia Clinica e Comportamentale, IRCCS Fondazione Santa Lucia, via Ardeatina 306 - 00179 Roma Tel. +39 (0)6 51501358 Fax +39 (0)6 90280774 web: http://www.neuropsichiatrialab.com<http://www.neuropsichiatrialab.com/it/personale/sabrina-fagioli>

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Freesurfer November 2013