Freesurfer

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30132 discussions

Re: [Freesurfer] hippo_subfields atlas
by Rajapillai Pillai 08 Aug '13

08 Aug '13

Hi again! I have another question about the hippocampal subfields atlas--might be a silly one. Is there a way to extract volumes from the mesh collection? Thanks a lot, Raja On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias < iglesias(a)nmr.mgh.harvard.edu> wrote: > Sounds good, but please email the list, rather than only me ;-) > /E > > > On 07/31/2013 05:03 PM, Rajapillai Pillai wrote: > > Thanks a lot. I'll let you know if I have any more issues. > > Best regards, > Raja > > > On Wed, Jul 31, 2013 at 4:44 PM, Juan Eugenio Iglesias < > iglesias(a)nmr.mgh.harvard.edu> wrote: > >> Did you run recon-all -subjid bert -hippo-subfields? If so, there should >> be a log file with the output from the hippo-subfield code in >> $SUBJECTS_DIR/bert/scripts/hippo-subfields.log. You can take a look at it >> to get an idea of what happened. >> Kind regards, >> /Eugenio >> >> >> On 07/31/2013 04:38 PM, Rajapillai Pillai wrote: >> >> Thanks very much for the prompt response. The command I ran was >> >> $ kvlQuantifyPosteriorProbabilityImages >> /Applications/freesurfer/data/GEMS/compressionLookupTable.txt >> posterior_right_* posterior_Right-Hippocampus.mgz >> >> in $SUBJECTS_DIR/bert/mri >> >> And yeah, it's not in the mri directory. Any idea what might have gone >> wrong and how I can try and fix it? >> >> Thanks, >> Raja >> >> >> On Wed, Jul 31, 2013 at 4:29 PM, Juan Eugenio Iglesias < >> iglesias(a)nmr.mgh.harvard.edu> wrote: >> >>> Hi Raja, >>> >>> >>> >>> I'm have a question regarding the GEMS hippocampal segmentation. I saw >>> on the wiki how to run -hippo_subfields, but how do I access the atlas >>> itself? What file is it under. >>> >>> >>> That would be $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz >>> >>> >>> >>> Also, I'm not sure if I'm missing some files: whenever I try to do one >>> of the individual commands using, for example, >>> posterior_Right_Hippocampus.mgz, it gives the following error: >>> >>> volumeInVoxels: >>> terminate called after throwing an instance of 'itk::ExceptionObject' >>> what(): itkMGHImageIO.cxx:216: >>> itk::ERROR: MGHImageIO(0x56b5c0): Can't find/open file: >>> posterior_Right-Hippocampus.mgz >>> Abort trap >>> >>> >>> What command is this? In any case, it's pretty clear that the file is >>> missing.... >>> >>> >>> Also, upon searching through my freesurfer directory, I cannot find >>> any posterior_Right-Hippocamus.mgz or posterior_Left-Hippocampus.mgz files. >>> >>> It should be under the "mri" directory. If it isn't, there was some >>> problem running the algorithms. >>> >>> Cheers, >>> >>> /Eugenio >>> >>> >>> >>> >>> >>> Thanks very much for your time, >>> Raja >>> >>> >>> _______________________________________________ >>> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> -- >>> ------------------------------------------------------------------------------------- >>> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >>> Athinoula A. Martinos Center for Biomedical Imaging >>> 149 Thirteenth Street, Suite 2301 >>> Charlestown, Massachusetts 2129 >>> U.S.A. >>> >>> 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. >>> >> >> >> -- >> ------------------------------------------------------------------------------------- >> Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu >> Athinoula A. Martinos Center for Biomedical Imaging >> 149 Thirteenth Street, Suite 2301 >> Charlestown, Massachusetts 2129 >> U.S.A. >> >> > > -- > ------------------------------------------------------------------------------------- > Juan Eugenio Iglesias, PhDhttp://www.jeiglesias.comiglesias@nmr.mgh.harvard.edu > Athinoula A. Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, Massachusetts 2129 > U.S.A. > >

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CUDA binaries
by Jordi Delgado 08 Aug '13

08 Aug '13

Dear freesurfers, I'm trying to exploit CUDA capabilities by using recon-all with -use-gpu. On the freesurfer wiki I found an approximate speedups for the main CUDA implementations in Freesurfer ( http://ftp.nmr.mgh.harvard.edu/fswiki/CUDADevelopersGuide) But I can't found mri_watershed_cuda and mri_ca_label_cuda on my freesurfer5.3/bin folder, and neither on previous versions. Are these implementations available? I tried to found the CUDA binaries on ( ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/) without luck. I know that CUDA support is no longer offered but it seems interesting to enable all the -cuda binaries executions to measure the improvement. And finally I would know if the cuda binaries offered in 5.3 version are compiled for a Fermi or Tesla? I hope that you are enjoying the summer! Kind regards,

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error when using selxavg3-sess in retinotopy analysis
by Sepide Movaghati 08 Aug '13

08 Aug '13

thank you for your respond. I create the subjectname file like the following: touch subjectname.txt echo "ZY" > $sessionDir/subjectname.txt now I removed the ".txt", and now I am getting this new error: outtop = /export01/data/sepid/subjects/ZY Extension format = nii.gz Error using MRIread (line 76) ERROR: cannot determine format of /export01/data/sepid/subjects/ZY/session1/bold/003/fmcpr.sm5.self.lh (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 ________________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Douglas N Greve [greve(a)nmr.mgh.harvard.edu] Sent: Wednesday, August 07, 2013 6:41 PM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] error when using selxavg3-sess in retinotopy analysis It is having problems reading the subjectname file in the session folder. Look in there to see if there is something obviously wrong. Did you create it on a windows computer? doug On 08/07/2013 04:16 PM, Sepide Movaghati wrote: > Hi, > > I followed the steps for doing the retinotopy analysis. At the end I > made my analysis as follows: > > mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy > 36-paradigm rtopy.par -fsd bold -fwhm 5 > > and then execute selxavg3-sess: > selxavg3-sess –a Retinotopy_ZY –s session1 > > then I got this error which I do not how to solve it: > > outtop = /export01/data/sepid/subjects/ZY > Extension format = nii.gz > Error using fscanf > Invalid file identifier. Use fopen to generate a valid file identifier. > > Error in flac_customize (line 47) > flacnew.sourcesubject = fscanf(fp,'%s',1); > > Error in fast_selxavg3 (line 65) > flac0 = flac_customize(flac0); > > >> ------------------------------------------ > ERROR: fast_selxavg3() failed\n > > > I would appreciate if you help me through this. > Regards, > Sepide > > - > > I > > > I > > - > > > > > > a > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 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(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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Re: [Freesurfer] Different results in surface and volume analyses
by Emily Boeke 08 Aug '13

08 Aug '13

Hi Doug, Thanks for the response. Is this masking out of the cortical regions in the volume analysis a newer aspect of the processing stream? Previously I have seen this activation in the volume. It would be great if you could let me know the flags to see the full volume analysis. Thanks! Emily Message: 41 Date: Wed, 07 Aug 2013 19:29:33 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Different results in surface and volume analyses To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <5202D85D.1090808(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Emily, the processing stream is designed to mask out cortical regions from the volume analysis. The volume analysis is used for subcortical structures. To make sure that the same voxels are not analyzed twice, the cortical surface is masked out of the mni305 analysis. doug ps. If you really want to see the full volume analysis, then there are some flags that will do this. Message: 14 Date: Wed, 7 Aug 2013 13:15:37 -0400 From: Emily Boeke <eboeke01(a)nmr.mgh.harvard.edu> Subject: [Freesurfer] Different results in surface and volume analyses To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <948E8FDF-754A-4AE0-A0C9-86D848F1438A(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=us-ascii Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in this region. These are the preprocess , mkanalysis, and selxavg commands I used for the surface vs. mni305: preproc-sess -s amur_dss -df sesspar -per-run -fwhm 5 -sliceorder down -surface fsaverage lhrh -mni305-2mm -fsd cond mkanalysis-sess -fsd cond -surface fsaverage lh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.lh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -surface fsaverage rh -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.rh -per-run -nskip 4 -stc down mkanalysis-sess -fsd cond -mni305 2 -fwhm 5 -paradigm Fear_Gen_Cond.par -event-related -TR 3 -nconditions 3 -polyfit 4 -spmhrf 0 -refeventdur 6 -analysis cond.sm05.mni305 -per-run -nskip 4 -stc down selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.lh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.rh selxavg3-sess -s amur_dss -df sesspar -analysis cond.sm.mni305 Why might we be seeing this activation on the surface map but not the volume one? Thanks! Emily

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(no subject)
by aqureshi＠nmr.mgh.harvard.edu 08 Aug '13

08 Aug '13

Hi Dr. Fischl, I had a couple subjects that failed recon-all. Although the error log said recon-all failed at mri_watershed it looks like the root problem is a couple steps earlier, because the nu.mgz looks too dark. This was discussed in a previous thread from 2008. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. You wrote, "p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes nu_correct can create very dark images, and there are some switches you can loo through to correct them. Alternatively if it is the 001.mgz, mri_convert has a scale option you can use." On my subject 001.mgz looks good (there was no 002.mgz file). It is only nu.mgz that looks too dark. It looks like the solution you gave then was for a problematic 001.mgz file, but from your response it looks as if the problem was nu.mgz the solution would be different. What are the switches you can loop through to correct the nu.mgz. Thanks, Abid

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monte carlo results differences between qdec and glmfit
by Marie Farstad Høvik 08 Aug '13

08 Aug '13

Dear Freesurfer experts, We are using mri_glmfit and wanted to compare our results to qdec to decide which method we prefer for group analysis. The results are consistent between the two methods, except for the monte carlo results. When we run mri_glmfit-sim to do the monte carlo simulations there are no significant clusters. We are not surprised by this as when we apply a FDR corrections all of our clusters go away. However, when we are using the monte carlo method in qdec we get a large significant cluster (in the csd summary file there are two large significant clusters, but using the image in qdec we only see one of them). The model is the same for both methods. We are (or think) we are using the exact same parameters as qdec. Is there a reason why the simulation results are so different? Which result should we use? The following are two of the simulation commands we have tried using v5.1: mri_glmfit-sim --glmdir glm/lh.asrs_sex_age.thickness.glmdir/ --sim mc-z 100 4 mc-z.unsigned --sim-sign abs --cwpvalthresh 0.01 --overwrite mri_glmfit-sim --glmdir glm/lh.asrs_sex_age.thickness.glmdir/ --sim mc-z 100 2 mc-z.unsigned --sim-sign abs --cwpvalthresh 0.01 --overwrite For the following command, we saw three clusters (they are inconsistent with the qdec ones), but none of them significant (p-values=.2): mri_glmfit-sim --glmdir glm/lh.asrs_sex_age.thickness.glmdir/ --sim mc-z 100 4 mc-z.unsigned --sim-sign abs --cwpvalthresh 0.995 --overwrite We haven't run 10 000 simulations yet, because we wanted to see if there were any significant clusters there at all before running that many simulations. Any advice would be very helpful. Thank you for your time, Marie

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CC mask
by Joao Pedro Battistella Nadas 08 Aug '13

08 Aug '13

> Hello, > > I am working with freesurfer to segment MRI images and I need to obtain a binary mask of the Corpus Callosum. Using the aseg.mgz file I was able to identify it segmented into 5 different structures (labels 251 to 255). However when looking at the mask of the union of those 5 labels, the CC does not look like the shape it should have (it looks like it is just the central part of it). I am trying to obtain this mask for the example patient "bert", and later on I will apply it to my own cases. > Any help would be much appreciated, > thank you > João Pedro B. Nadas

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mri_cvs_register for EPI
by Marcel Falkiewicz 08 Aug '13

08 Aug '13

Hello, I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resoluton (for subsequent ICA analysis). I'm taking following steps: 1. recon-all on anatomical data (obvious) 2. mri_cvs_register (mri_cvs_register --targ cvs_avg35_inMNI152 --mov subject) I do not understand what the files stored in cvs folder are needed for. As far as I understand the normalization process, I need a file which stores the subject -> template warp. Which file is it? Do I need to use the --nocleanup option in mri_cvs_register to get the aforementioned file? In the wiki page a following command line is recommended to reconstruct this warp when the --nocleanup options was not used: createMorph --out fullCVSmorph.tm3d --template template.mgz \ - --subject movingvol.mgz --in gcam nlalign-afteraseg-norm.m3z \ morph el_reg_toTEMPLATE.tm3d However, there is no single *.tm3d file in my cvs directory... Here are the files that are present: el_reg_tocvs_avg35_inMNI152.affine.mgz el_reg_tocvs_avg35_inMNI152_aseg.mgz el_reg_tocvs_avg35_inMNI152.mgz final_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz final_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz final_CVSmorph_tocvs_avg35_inMNI152.m3z lh.dbg_surf.pial lh.dbg_surf.white lh.resample.aparc.annot lh.resample.pial lh.resample.white nlalign-afteraseg-norm.mgz nlalign-aseg.mgz rh.dbg_surf.pial rh.dbg_surf.white rh.resample.aparc.annot rh.resample.pial rh.resample.white step1_CVSmorphed_tocvs_avg35_inMNI152_aseg.mgz step1_CVSmorphed_tocvs_avg35_inMNI152_norm.mgz summary.AC1004_to_cvs_avg35_inMNI152.mri_cvs_register.1308031447.log transform.txt In my particular case, which images should be entered as arguments to --template and --subject ? 3. standard EPI pre-processing, which results in motion-correction parameters and realigned images 4. coregistration of EPI to anatomical data with BBR. The transformation is stored as register.dof6.dat, which contain the mapping EPI -> anatomical I understand that the next step is combining the registrations from step (2) and (4) in order to get EPI images in cvs_MNI space. This can be accomplished with mri_vol2vol. However, I do not understand which files should be used for this registration. Sorry for the lenghty post, but I'm quite new to freesurfer and I'm a bit confused:) Best regards, Marcel

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Re: [Freesurfer] (no subject)
by Bruce Fischl 08 Aug '13

08 Aug '13

you could try using --scale <scale factor> to scale the intensities of the 001.mgz up On Wed, 7 Aug 2013, Abid Qureshi wrote: > I'm using 4.5.0. The earliest subjects were done using 4.5.0 so for consistency we are sticking with 4.5.0. - > Abid > > > On Wed, Aug 7, 2013 at 6:52 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > Hi Abid > > what version of FS are you using? > Bruce > On Wed, 7 Aug 2013, aqureshi(a)nmr.mgh.harvard.edu wrote: > > Hi Dr. Fischl, > > I had a couple subjects that failed recon-all. Although the error log said > recon-all failed at mri_watershed it looks like the root problem is a > couple steps earlier, because the nu.mgz looks too dark. This was > discussed in a previous thread from 2008. > > http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07293.html. > > You wrote, "p.s. are the 001.mgz and 002.mgz dark? The orig.mgz? Sometimes > nu_correct can create very dark images, and there are some switches you > can loo through to correct them. Alternatively if it is the 001.mgz, > mri_convert has a scale option you can use." > > On my subject 001.mgz looks good (there was no 002.mgz file). It is only > nu.mgz that looks too dark. It looks like the solution you gave then was > for a problematic 001.mgz file, but from your response it looks as if the > problem was nu.mgz the solution would be different. What are the switches > you can loop through to correct the nu.mgz. > > Thanks, > Abid > > _______________________________________________ > 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. > > > > > -- > WARNING: E-mail sent over the Internet is not secure. Information sent by e-mail may not remain confidential. > > DISCLAIMER: This e-mail is intended only for the individual to whom it is addressed. It may be used only in > accordance with applicable laws. If you received this e-mail by mistake, notify the sender and destroy the > e-mail > >

1 0

Group analysis
by Marcos Martins da Silva 08 Aug '13

08 Aug '13

Hi, FreeSurfers. Is it possible to use FreeSurfer's group analysis tools to investigate surface deformation instead of thickness? I guess it would be interesting for subcortical structures like putamen, amygdala or hippocampus. Let's say you get the putamen data from 15 subjects and compare it to putamen data from fsaverage, After correct registration, I guess we can detect regions of contraction and expansion leading to changes in the putamen contour. I imagined it could be done if we calculate the signed Euclidean distances between the corresponding points of for each subject's putamen and fsaverage, with positive and negative values indicating, for example, the presence of an outward or inward surface deformation. After all calculation I guess we can get a similar result to the pictures we can see at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis but showing only a putamen and the colors meaning surface deformation instead of thickness. This way, you can notice morphological differences among subjects even if they have the same volume. Thanks in advance, Marcos

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