[Freesurfer] creating labels, new atlas
Hello, How can tksurfer be used to create label files for the purpose of making a new atlas, if that atlas is needed to create the surface files needed to view the brain in tksurfer? Would people use FSL to create the masks, and convert them into what is needed for freesurfer or is there another way? Thank you, Jeff Thompson ___ 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] FDR Correction of NHP Surface Data
Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark ___ 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] How to Convert QDEC clusters to standard MNI_152_T1 space
Hi Doug, Many thanks for your help. Can you please take a look and see if this is the correct way to do it. I want to overal in fact my QDEC clusters on the connectivity maps in FSL but I got them by registering on the MNI 152 so I suppose I can just transform or move my QDEC clusters on the MNI space since this is the template I use for my connectivity maps. I am not sure how I can mention the label of my clusters, the uncorrected clusters. Should I use the sig.mgh as subject id, my clusters were obtained from all my subjects or it should be the fsaverage? How I can identify the label of my clusters more exactly how I can keep only the clusters (name and size) from QDEC as in thefollowing table or where I can find for each QDEC's cluster the label so I can use it under --label option ? mri_label2vol --label ??? --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh .5 --subject /lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh --hemi lh --o precentral-lh.nii Also is the 0.5 the threshold I need to use with mri_label2vol under option --fillthresh if I want to get my uncorrected clusters? How can I do this if as below I have two clusters in the same region? Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation - --- -- - - -- 1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral 2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal 3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal 4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula 5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine 6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal 7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole 8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal 9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral 10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198 posteriorcingulate 11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal 12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal 13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts 14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal 15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal 16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis 17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal 18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital 19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral 20 -2.0221 19174 4.10 -34.2 33.8 29.2 6 rostralmiddlefrontal From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: Dear All, Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template? Thank you. Antonella ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.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.___ 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
[Freesurfer] resending question about 3rd level analysis
Hi, I'm resending this e-mail, as it didn't seem to go through correctly yesterday: I’m a Freesurfer novice, and I’m confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis in FSL. Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using mris_preproc. I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using: mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label However, I want to use a random as opposed to fixed effects analysis. How do I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And if I’m going to display the map resulting from this analysis, do I need to correct for multiple comparisons? Many thanks in advance, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington ___ 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] qdec generate stats data tables
I am trying to use the generate stats data tables feature in qdec but am getting the error message below. So based on the error message I know that the trouble subject is SZ0020 and I looked in his file and found the attached aseg.stats file, which looks okay. I reven tried rerunning the segstats using recon-all -s SZ0020TS/ -segstats. Any ideas? asegstats2table --common-segs --meas volume --tablefile /Applications/freesurfer/subjects/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects SZ_0020 SZ_0030 SZ_0033 SZ_0045 SZ_0049 SZ_0050 SZ_0058 SZ_0067 SZ_0006 SZ_0037 SZ_0038 SZ_0040 SZ_0048 SZ_0051 SZ_0053 SZ_0054 SZ_0059 SZ_0060 SZ_0062 SZ_0065 SZ_0069 SZ_0071 SZ_0072 SUBJECTS_DIR : /Applications/freesurfer/subjects Parsing the .stats files ERROR: The stats file /Applications/freesurfer/subjects/*SZ_0020*/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files Take care, Nathan Hutcheson Graduate Research Assistant 501 Sparks Center 1748 7th Ave South Birmingham, AL 35233 aseg.stats 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.
Re: [Freesurfer] creating labels, new atlas
I found this info on the tksurfer webpage. The label file format is interchangable with TkMedit. You can create a label in TkSurfer, save it, and load it in TkMedit, or vice versa. Jeff Thompson From: jeff_rthomp...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: creating labels, new atlas Date: Thu, 23 Aug 2012 10:48:46 -0300 Hello, How can tksurfer be used to create label files for the purpose of making a new atlas, if that atlas is needed to create the surface files needed to view the brain in tksurfer? Would people use FSL to create the masks, and convert them into what is needed for freesurfer or is there another way? Thank you, Jeff Thompson ___ 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] creating a gca file from .mgz files
From the gcaFormat freesurfer wiki page I know that: The .gca file is composed of three volumes, which can be extracted like this:mri_convert atlas.gca -nth 0 means.mgz mri_convert atlas.gca -nth 1 labels.mgz mri_convert atlas.gca -nth 2 priors.mgzwhere:means -- the mean intensity of the most likely labellabels -- indices of the most likely label at each voxel (indices refer to '#No.' column of $FREESURFER_HOME/FreeSurferColorLUT.txt)priors -- the probability that that label occurs at that voxel Is it possible to go the other way? I want to create the labels.mgz file and the others manually, and turn that into the .gca file with mri_convert. Can this be done? Thank you, Jeff Thompson ___ 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] REPOST: How to Convert QDEC clusters to standard MNI_152_T1 space
Hi, I want to overal my QDEC clusters on the connectivity maps in FSL on the MNI ( this is the template I use for my connectivity maps). I am not sure how I can mention the label of my clusters, the uncorrected clusters. Should I use the sig.mgh as subject id, my clusters were obtained from all my subjects or it should be the fsaverage? Should I use mri_label2vol or mri_surf2vol? How I can identify the label of my clusters more exactly how I can keep only the clusters (name and size) from QDEC as in thefollowing table or where I can find for each QDEC's cluster the label so I can use it under --label option ? mri_label2vol --label ??? --temp MNI152_T1_1mm_brain.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --fillthresh .5 --subject /lh-Diff-Class1-Class2-Intercept-thickness/sig.mgh --hemi lh --o precentral-lh.nii Also is the 0.5 the threshold I need to use with mri_label2vol under option --fillthresh if I want to get my uncorrected clusters? How can I do this if as below I have two clusters in the same region? Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation - --- -- - - -- 1 -3.8743 18231 944.60 -39.8 1.5 14.1 2631 precentral 2 -3.8065 47386 1445.46 -8.2 33.1 33.9 2421 superiorfrontal 3 -2.8630 158749 181.92 -12.7 -12.6 46.4 506 superiorfrontal 4 -2.7960 73670 222.37 -33.7 0.9 8.1 564 insula 5 2.7914 52279 204.80 -9.8 -98.6 4.6 248 pericalcarine 6 -2.7364 43605 173.45 -41.4 -79.2 21.8 288 inferiorparietal 7 -2.6316 17412 301.53 -38.3 5.6 -36.8 439 temporalpole 8 2.6050 150788 64.40 -24.0 -59.1 54.7 165 superiorparietal 9 -2.5570 106020 75.96 -22.8 -8.6 47.9 200 precentral 10 -2.5070 88002 66.59 -17.6 -31.2 37.8 198 posteriorcingulate 11 -2.4736 113974 181.87 -52.7 -10.3 -26.6 236 middletemporal 12 -2.4496 118370 142.88 -43.6 -18.0 -25.5 289 inferiortemporal 13 -2.3087 111885 55.43 -46.6 -36.2 -3.9 165 bankssts 14 -2.2179 153596 36.91 -11.3 3.4 42.0 103 superiorfrontal 15 -2.1861 145681 95.36 -11.3 60.1 19.1 147 superiorfrontal 16 -2.1733 29252 59.92 -42.6 37.5 -4.4 92 parstriangularis 17 -2.1689 155583 34.83 -45.3 -14.7 -11.2 87 superiortemporal 18 -2.1636 22443 27.76 -41.6 -79.0 -3.1 43 lateraloccipital 19 -2.1592 139736 21.75 -47.5 -25.1 37.0 61 postcentral 20 -2.0221 19174 4.10 -34.2 33.8 29.2 6 rostralmiddlefrontal From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, August 21, 2012 4:55 PM Subject: Re: [Freesurfer] Convert QDEC clusters on the MNI_152_T1 space You can use mri_label2vol and $FREESURFER_HOME/average/mni152.register.dat doug On 08/21/2012 11:06 AM, Antonella Kis wrote: Dear All, Is possible to overlap my QDEC clusters onto MNI_152_T1 _1mm_brain template? Thank you. Antonella ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.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.___ 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] Tracula question
Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm T1 MNI template (i tried using the 2mm one but the vertices for registering white matter came out as NaN). However, I was not able to get bedpost to work. After looking at other posts on the FS archive, I think the reason why -bedp does not work is because of my FSL version. I tried running bedpost on FSL and then just copying those files on my dmri.bedpost folder and using those files for reconstructing the white matter tracts. However, I get a Segmentation Fault error. Do you have any idea what this error may mean? My dpath folder is empty and I my trac-all.log file has no errors related to -path Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is bet - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wrote: The required files were not generated. the error occurs at rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni/low b_brain _mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dmri/mni/dtifit_F A.fl t.nii.gz --ncpts 5 --trunc --debug ERROR: fio_pushd: /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni ERROR: Must specify brain mask volume for output subject does the brain mask have to be input manually in the configuration file, or is this part of the pre-processing? since I set the bet thr to 0.23 in the config file i thought the brain mask was also created during the preprocessing stage. Attached is my log file. I am familiar with FSL but I am using Free surfer since i think automating the entire process, including tracking is a great advantage, but I'm just starting to get the hang of it Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 4:28 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: dtifit_FA.fl t.nii.gz 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.
Re: [Freesurfer] Tracula question
Can you please check that the x-y-z dimensions of the bedpostx output files are the same as the dimensions of the DWIs? On Thu, 23 Aug 2012, Natalia Sánchez wrote: Thanks for your response!Attached are the requested files The error occurs here are shown on my terminal: Loading b-values from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv als Loading gradients from/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmri/bv ecs Segmentation fault Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm T1 MNI template (i tried using the 2mm one but the vertices for registering white matter came out as NaN). However, I was not able to get bedpost to work. After looking at other posts on the FS archive, I think the reason why -bedp does not work is because of my FSL version. I tried running bedpost on FSL and then just copying those files on my dmri.bedpost folder and using those files for reconstructing the white matter tracts. However, I get a Segmentation Fault error. Do you have any idea what this error may mean? My dpath folder is empty and I my trac-all.log file has no errors related to -path Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is bet - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez wrote: The required files were not generated. the error occurs at rh.slft_PP_roi2.flt.nii.gz--bmask/Users/Natalia/Desktop/freesurfer/subjects /Justin/cJD/dlabel/mni/low b_brain _mask.flt.nii.gz--fa/Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/d mri/mni/dtifit_F A.fl t.nii.gz --ncpts 5 --trunc --debug ERROR: fio_pushd: /Users/Natalia/Desktop/freesurfer/subjects/Justin/cJD/dlabel/mni ERROR: Must specify brain mask volume for output subject does the brain mask have to be input manually in the configuration file, or is this part of the pre-processing? since I set the bet thr to 0.23 in the config file i thought the brain mask was also created during the preprocessing stage. Attached is my log file. I am familiar with FSL but I am using Free surfer since i think automating the entire process, including tracking is a great
[Freesurfer] Whole Brain Volume
Hello All, We are looking into alternative measures for whole brain volume to use for covarying, and the previous topic mentioned mris_volume as a possibility but it isn't located on the top of the aseg file. Has it been moved? Chris McCarthy ___ 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] Tracula question
This probably means that bedpostx didn't process all the slices in your DWIs. Someone else reported something like that recently, not sure what may be causing it, but since it's independent of trac-all, I'd check on the FSL list archives. On Thu, 23 Aug 2012, Natalia Sánchez wrote: they are not. The z dimension of the bedpost images is 52 (from FSL) and for the dmri FS images it is 72. -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Thu, Aug 23, 2012 at 2:08 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Can you please check that the x-y-z dimensions of the bedpostx output files are the same as the dimensions of the DWIs? On Thu, 23 Aug 2012, Natalia Sánchez wrote: Thanks for your response!Attached are the requested files The error occurs here are shown on my terminal: Loading b-valuesfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr i/bv als Loading gradientsfrom/Users/Natalia/Desktop/freesurfer/subjects/Justin/diff_tutorial/cJD/dmr i/bv ecs Segmentation fault Darwin dhcp-165-124-9-141.phystherapy.northwestern.edu 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun 7 16:33:36 PDT 2011; root:xnu-1504.15.3~1/RELEASE_I386 i386 -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Thu, Aug 23, 2012 at 1:48 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Natalia - I'd need to see at which point in the processing the error occurs, since this is a very generic error message. Can you please include your trac-all.log and dmrirc? Thanks, a.y On Thu, 23 Aug 2012, Natalia Sánchez wrote: Hi Anastasia!I finally made tracula -prep work without errors, using the 1mm T1 MNI template (i tried using the 2mm one but the vertices for registering white matter came out as NaN). However, I was not able to get bedpost to work. After looking at other posts on the FS archive, I think the reason why -bedp does not work is because of my FSL version. I tried running bedpost on FSL and then just copying those files on my dmri.bedpost folder and using those files for reconstructing the white matter tracts. However, I get a Segmentation Fault error. Do you have any idea what this error may mean? My dpath folder is empty and I my trac-all.log file has no errors related to -path Thanks! -- Natalia Sánchez PhD Candidate Departments of Biomedical Engineering Physical Therapy and Human Movement Sciences Northwestern University 645 North Michigan Ave, Suite 1100 Chicago, IL 60611 On Fri, Aug 10, 2012 at 5:05 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Natalia - This is an error that will occur if lowb_brain_mask does not exist. The command that generates lowb_brain_mask is bet - can you find that line in the log file and run it directly on the command line and see if you get an error? On a separate note, have you opted to use a DWI mask instead of an anatomical mask by setting usemaskanat = 0? If not, then it may be that it's trying to use the DWI mask b/c it can't find the anatomicals, in which case I'd check if SUBJECTS_DIR has been set properly and a freesurfer recon of the same subject exists there. But this is a separate issue than the DWI mask not being generated. Hope this helps, a.y On Fri, 10 Aug 2012, Natalia Sánchez
[Freesurfer] Surface statistics for PET
I would like to calculate average PET intensities for specific labels (using the aparc.annot label files). I have coregistered and used mri_vol2surf to assign PET values to the FS generated surface, and viewed the results using qsurfer. The next step is to take the values from the .w files and calculate label-specific stats. I've tried mris_anatomical_stats but I don't think this is the right command. Any advice? Thank you in advance, Daniel ___ 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] mri_segstats error
Hi, Doug and all, I wonder if the new version of mri_segstats on the ftp site will change both the ICV and the SupraTentorial volume? Nick seems to mention ICV will be different, the ReleaseNotes says the SupraTentorial Volume will be changed to smaller. Can you explain more on the difference of the new version with the original version in FS.5.1.0? Is everything on the morphometry stats website still the same? http://surfer.nmr.mgh.harvard.edu/fswiki/MorphometryStats. I'm interested in several measurements, including the ICV, and the SupraTentorial Volume and all the structures volume, just wondering if the new version will change all the measurements. Thanks. -Natalie On Wed, Aug 22, 2012 at 8:57 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: yes, this is a fix that will be in the next release. The new results are more accurate. doug On 08/22/2012 11:54 AM, Blazey, Tyler wrote: Hi Doug, Thanks for the quickly reply. The new version of mri_segstats works fine. I noticed after running it though that all the volumes are slightly different than those reported by previous version. I think it might have something to do with the partial volume correction, as the results are the same when I do not use the --pv flag. Is this expected behavior? And if so, is the new version more accurate? Thanks again, -Tyler The material in this message is private and may contain Protected Healthcare Information (PHI). If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] repeated measures ANOVA with two groups
Hi, Is there a way to set up a repeated measures ANOVA and ANCOVA with two different groups (ex: study group v. controls) and each subject has more than two timepoints? Would it be possible to assign each Input in the fsgd file to two classes (ex: timepoint scan and group) or is there another way to set up the fsgd file and contrast matrices? I've already used qdec in freesurfer 5.1 to calculate rates of change and symmetrized percent changes between the timepoints (using long_mris_slopes) but now would like to perform a repeated measures test. Thank you! -Shannon K. ___ 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.
