Re: [Freesurfer] error mris_anatomicalstats
Dear Bruce, I first used the example command line from the wiki: mri_annotation2label --subject LW \ --hemi rh --outdir ./labels(on my own subject) and then used mri_mergelabels -i lh.entorhinal.label -i lh.cuneus.label -o test.label I use Freesurfer 5.1 on Linux system. Are commands incorrect any stage? If so could you direct please me to correct ones? Kind Regards, Linn On Mon, Mar 25, 2013 at 12:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Linn can you send us the exact command line and screen output, and also what version and software/hardware environment you are running in? cheers Bruce On Mon, 25 Mar 2013, Linn Mittlestein wrote: Dear Freesurfer experts, I have a question about trying to extract statistics from merged labels using mris_anatomical_stats. I have used the mri_annotation2label, and then the mri_merge label, however now when trying to do mris_anatomical stats, I get the error ; could not read input volume, eg Freesurfer cannot read the wm.mgz file. What step have I done wrong? Thank you very much, Kind Wishes, Linn 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/**compliancelinehttp://www.partners.org/complianceline. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: Re: R: Re: hippo subfield
Hi Zeke and other users, I have finished the Hippocampal Subfields parcellation. New files .mgz are located in $SUBJECTS_DIR/mri. Now, I do not understand as I can calculate for each region the thickness and volume. Can you help me, please? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, std...@virgilio.it wrote: Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfields Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: Diff01 side: left inputDirectory: /Applications/freesurfer/subjects/subject_prova outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already exists directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already exists cd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.0330 0.9994 -0.00862.65600.02550.0094 0.9996 -3.1939 Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 20.53 A: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Stefano, In order to fix this issue please follow these instruction exactly: 1) Download the file kvl.zip from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ 2) Overwrite the existing kvl files in /Application/freesurfer/bin with the files in kvl.zip I was able to replicate your issue and solve it using the steps above. If these steps do not solve the issue for you, please respond with a the exact error you receive. Hope this helps. -Zeke On 03/22/2013 12:00 PM, std...@virgilio.it wrote: I'm running: recon-all -s Diff02 -hippo-subfields with the
[Freesurfer] surf2vol
Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template path to/orig.mgz --outvol path to where I want the file/leftfrontallobe.nii.gz --surfval path to/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan Date: Mon, 25 Mar 2013 14:59:28 -0400 From: fis...@nmr.mgh.harvard.edu To: doclums...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surf2vol Hi Dan try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote: Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow 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] error mris_anatomicalstats
Hi Linn what was your mris_anatomical_stats commandline? Bruce On Tue, 26 Mar 2013, Linn Mittlestein wrote: Dear Bruce, I first used the example command line from the wiki: mri_annotation2label --subject LW \ --hemi rh --outdir ./labels(on my own subject) and then used mri_mergelabels -i lh.entorhinal.label -i lh.cuneus.label -o test.label I use Freesurfer 5.1 on Linux system. Are commands incorrect any stage? If so could you direct please me to correct ones? Kind Regards, Linn On Mon, Mar 25, 2013 at 12:51 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Linn can you send us the exact command line and screen output, and also what version and software/hardware environment you are running in? cheers Bruce On Mon, 25 Mar 2013, Linn Mittlestein wrote: Dear Freesurfer experts, I have a question about trying to extract statistics from merged labels using mris_anatomical_stats. I have used the mri_annotation2label, and then the mri_merge label, however now when trying to do mris_anatomical stats, I get the error ; could not read input volume, eg Freesurfer cannot read the wm.mgz file. What step have I done wrong? Thank you very much, Kind Wishes, Linn The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] qdec matrix error
Hi, I'm performing qdec. This my file.dat 1 diagnosis discrete 21 Pathology2 Controls2 Thickness_lh continuous 03 Thickness_rh continuous 04 NPStest continuous 0 Continuous Factors: Mean: StdDev: --- - --- Thickness_lh 2.643 0.116 Thickness_rh 2.630 0.099 NPStest 0.774 1.203 Number of subjects: 31Number of factors:4 (1 discrete, 3 continuous)Number of classes:2Number of regressors: 8 NPStest is scored from 0 to 8. Qdec produces this error: Creating output directory /Applications/freesurfer/subjects/subject_prova/qdec/UntitledLoading y from /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mghINFO: gd2mtx_method is dodsSaving design matrix to /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/Xg.datNormalized matrix condition is 1e+08Design matrix -- 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.712 0.000; 1.000 0.000 0.000 0.000 2.671 0.000; 1.000 0.000 0.000 0.000 2.728 0.000; 1.000 0.000 0.000 0.000 2.646 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.750 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.784 0.000; 1.000 0.000 0.000 0.000 2.586 0.000; 1.000 0.000 0.000 0.000 2.641 0.000; 1.000 0.000 0.000 0.000 2.561 0.000; 1.000 0.000 0.000 0.000 2.545 0.000; 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.769 0.000; 1.000 0.000 0.000 0.000 2.740 0.000; 0.000 1.000 0.000 2.000 0.000 2.526; 0.000 1.000 0.000 2.000 0.000 2.761; 0.000 1.000 0.000 2.000 0.000 2.521; 0.000 1.000 0.000 0.000 0.000 2.592; 0.000 1.000 0.000 2.000 0.000 2.555; 0.000 1.000 0.000 2.000 0.000 2.671; 0.000 1.000 0.000 3.000 0.000 2.559; 0.000 1.000 0.000 3.000 0.000 2.469; 0.000 1.000 0.000 4.000 0.000 2.691; 0.000 1.000 0.000 2.000 0.000 2.522; 0.000 1.000 0.000 0.000 0.000 2.553; 0.000 1.000 0.000 2.000 0.000 2.702; 0.000 1.000 0.000 0.000 0.000 2.738; 0.000 1.000 0.000 0.000 0.000 2.789; 0.000 1.000 0.000 0.000 0.000 2.651;ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08Possible problem with experimental design:Check for duplicate entries and/or lack of range ofcontinuous variables within a class.If you seek help with this problem, make sure to send: 1. Your command line:mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat 2. The FSGD file (if using one) 3. And the design matrix aboveError in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat I don't understand what's happen? Thanks, Stefano___ 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
Re: [Freesurfer] R: Re: R: Re: hippo subfield
Ciao, Stefano to compute subfield volumes, you need to use the script kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are here: http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation In the wiki page you'll also find instructions to visualize the output. Cheers, /Eugenio On Tue, March 26, 2013 4:40 am, std...@virgilio.it wrote: Hi Zeke and other users, I have finished the Hippocampal Subfields parcellation. New files .mgz are located in $SUBJECTS_DIR/mri. Now, I do not understand as I can calculate for each region the thickness and volume. Can you help me, please? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, std...@virgilio.it wrote: Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfields Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: Diff01 side: left inputDirectory: /Applications/freesurfer/subjects/subject_prova outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already exists directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already exists cd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.02550.00940.9996 -3.1939 Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 20.53 A: std...@virgilio.it, freesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] hippo subfield Stefano, In order to fix this issue please follow these instruction exactly: 1) Download the file kvl.zip from this link: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/ 2) Overwrite the existing kvl files in /Application/freesurfer/bin with the files in kvl.zip I was able to replicate your issue and solve it using the steps above.
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
Hi, I run the command for each BA labels of the right hemisphere and then run: [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white Which resulted in: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory What is wrong? Is there a way to run everything that is needed to get the BA stats at once using the BAxxx.thresh.label? Thank you, Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output. Run *all* the commands from the BA labels section, all the way to the end of that section, this will get you to the stats. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold? Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new filesaren't being used in 5.0. You'll need to find the BA labels section in recon-all.logand rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area andvolume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer freesurfer@nmr.mgh.harvard.edu Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu Hi all, I want to study Brodmann Areas cortical thickness, surface area and volume. I've added the 5.2 BAxxx.threshold.label to my 5.0 fsaverage and run the recon-all BA labels command. Now I run aparcstats2table and get a table with the values but they are the same as before running the BAxxx.threshold.label. So, everything is working but the values haven't changed. Am Imissing
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
Nevermind the last email... If I change the output (wich is the second place where BAxx.label appears, right?) file name and give the subjs id this won't be a problem... Anyway, what are these files for? Will I need to use them somehow? Thanks Andreia Quoting _andre...@sapo.pt: Addicionaly, this approach is creating an individual file for each BAxxx.thresh.label (see atchment) and I think that if I run these commands for another subject these outputs will be replaced since the name of the files has no info relating to the subject who it belongs. I'm kind of lost here... Quoting _andre...@sapo.pt: Hi, I run the command for each BA labels of the right hemisphere and then run: [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white Which resulted in: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory What is wrong? Is there a way to run everything that is needed to get the BA stats at once using the BAxxx.thresh.label? Thank you, Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output. Run *all* the commands from the BA labels section, all the way to the end of that section, this will get you to the stats. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold? Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new filesaren't being used in 5.0. You'll need to find the BA labels section in recon-all.logand rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt - Data: Sun, 24 Mar 2013 19:11:13 + De: _andre...@sapo.pt Assunto: Re: [Freesurfer] Brodmann area thickness, surface area andvolume Para: Anastasia Yendiki ayend...@nmr.mgh.harvard.edu, freesurfer
[Freesurfer] preproc-sess -surface flag
Hi, I wonder if you could help with a basic question for preproc-sess in Version 5.2.0. The flag -surface subject hemi: what should be the entry to subject? The tutorial says fsaverage, but for first-level analysis, should it match subjectname? Or should it always be fsaverage? If it needs to match subjectname, then this command cannot be run in a batch (because different subjects have different input to that line), is that true? Thank you. -Yuhong ___ 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] Cortical thickness in average space
Hi Freesurfers, We would need to obtain the cortical thickness of each subject in the space of the average subject (built from our subject population), Does it exists? If so, Can I use the label files produced by mri_surfcluster to directly extract the mean cortical thickness of each ROI in each subject? We want to avoid to trasform each cluster to every subject. Thank you all in advance, Rafa Gabi. ___ 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] Fwd: Brodmann area thickness, surface area and volume
In the BA label section there are: - Several mri_label2label commands that map each label from fsaverage space to your indidvidual's space - One mris_label2annot command that combines the mapped label into an annotation file. - One mris_anatomical_stats command that gets stats for that annotation. For each of these commands you can run them with --help to see what the inputs and outputs are, or look them up on the wiki. On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: Nevermind the last email... If I change the output (wich is the second place where BAxx.label appears, right?) file name and give the subjs id this won't be a problem... Anyway, what are these files for? Will I need to use them somehow? Thanks Andreia Quoting _andre...@sapo.pt: Addicionaly, this approach is creating an individual file for each BAxxx.thresh.label (see atchment) and I think that if I run these commands for another subject these outputs will be replaced since the name of the files has no info relating to the subject who it belongs. I'm kind of lost here... Quoting _andre...@sapo.pt: Hi, I run the command for each BA labels of the right hemisphere and then run: [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white Which resulted in: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory What is wrong? Is there a way to run everything that is needed to get the BA stats at once using the BAxxx.thresh.label? Thank you, Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output. Run *all* the commands from the BA labels section, all the way to the end of that section, this will get you to the stats. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold? Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or directory mri_label2label: could not open label file /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Illegal seek ERROR reading /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label Thus, I substitued only in the second BAxxx.label and it worked. I thought that was it, but then the values were the same. I'm sorry, I'm not sure what is missing. Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: Hi Andreia - What you're rerunning is using BAxxx.label instead of BAxxx.thresh.label. So of course the results will be the same as before you copied over the BAxxx.thresh.label files, b/c these new filesaren't being used in 5.0. You'll need to find the BA labels section in recon-all.logand rerun those commands yourself, changing every BAxxx.label to BAxxx.thresh.label. Hope this helps, a.y On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hello list! Any suggestions on what I may be doing wrong? Thanks! Andreia - Mensagem encaminhada de _andre...@sapo.pt -
Re: [Freesurfer] Incomplete and poorly formed tracts
Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH 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/**compliancelinehttp://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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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] R: Re: R: Re: R: Re: hippo subfield
Thank you very much Eugenio. I have a last question: Who is the best way to normalize the HippocampalSubfieldSegmentation volume results? Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 26-mar-2013 14.37 A: std...@virgilio.it Cc: zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield Ciao, Stefano to compute subfield volumes, you need to use the script kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are here: http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation In the wiki page you'll also find instructions to visualize the output. Cheers, /Eugenio On Tue, March 26, 2013 4:40 am, std...@virgilio.it wrote: Hi Zeke and other users, I have finished the Hippocampal Subfields parcellation. New files .mgz are located in $SUBJECTS_DIR/mri. Now, I do not understand as I can calculate for each region the thickness and volume. Can you help me, please? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, std...@virgilio.it wrote: Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfields Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: Diff01 side: left inputDirectory: /Applications/freesurfer/subjects/subject_prova outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already exists directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already exists cd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.02550.00940.9996 -3.1939 Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 For more details, see the log file /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 22-mar-2013 20.53 A: std...@virgilio.it,
Re: [Freesurfer] R: Re: R: Re: R: Re: hippo subfield
I would say intracranial volume from the aseg.stat table Cheers, /Eugenio On Tue, 2013-03-26 at 16:49 +0100, std...@virgilio.it wrote: Thank you very much Eugenio. I have a last question: Who is the best way to normalize the HippocampalSubfieldSegmentation volume results? Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 26-mar-2013 14.37 A: std...@virgilio.it Cc: zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield Ciao, Stefano to compute subfield volumes, you need to use the script kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are here: http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation In the wiki page you'll also find instructions to visualize the output. Cheers, /Eugenio On Tue, March 26, 2013 4:40 am, std...@virgilio.it wrote: Hi Zeke and other users, I have finished the Hippocampal Subfields parcellation. New files .mgz are located in $SUBJECTS_DIR/mri. Now, I do not understand as I can calculate for each region the thickness and volume. Can you help me, please? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, std...@virgilio.it wrote: Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfields Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: Diff01 side: left inputDirectory: /Applications/freesurfer/subjects/subject_prova outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already exists directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already exists cd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.00862.6560 0.02550.00940.9996 -3.1939 Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 recon-all -s Diff01 exited with ERRORS at Fri Mar 22 23:56:49 CET 2013 For more details, see the log file
Re: [Freesurfer] Cortical thickness in average space
Hi Rafa and Gabi yes, that's pretty much what the -qcache flag does in recon-all. Or you can use mri_surf2surf to do it. cheers Bruce On Tue, 26 Mar 2013, Rafa X wrote: Hi Freesurfers, We would need to obtain the cortical thickness of each subject in the space of the average subject (built from our subject population), Does it exists? If so, Can I use the label files produced by mri_surfcluster to directly extract the mean cortical thickness of each ROI in each subject? We want to avoid to trasform each cluster to every subject. Thank you all in advance, Rafa Gabi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Cortical thickness in average space
Or mris_preproc if you want all your subjects in one file. doug On 03/26/2013 12:13 PM, Bruce Fischl wrote: Hi Rafa and Gabi yes, that's pretty much what the -qcache flag does in recon-all. Or you can use mri_surf2surf to do it. cheers Bruce On Tue, 26 Mar 2013, Rafa X wrote: Hi Freesurfers, We would need to obtain the cortical thickness of each subject in the space of the average subject (built from our subject population), Does it exists? If so, Can I use the label files produced by mri_surfcluster to directly extract the mean cortical thickness of each ROI in each subject? We want to avoid to trasform each cluster to every subject. Thank you all in advance, Rafa Gabi. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] preproc-sess -surface flag
Thanks Doug, this makes sense. What about retinotopic mapping? Should I use fsaverage or self? -Yuhong On Tue, Mar 26, 2013 at 10:56 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It should either be fsaverage, or self, or an average subject you have created. The fMRI analysis is done such that the raw data are resampled into the fsaverage space (unless you use self) and processed there in anticipation of doing group analysis. doug On 03/26/2013 10:37 AM, Y.V. Jiang wrote: Hi, I wonder if you could help with a basic question for preproc-sess in Version 5.2.0. The flag -surface subject hemi: what should be the entry to subject? The tutorial says fsaverage, but for first-level analysis, should it match subjectname? Or should it always be fsaverage? If it needs to match subjectname, then this command cannot be run in a batch (because different subjects have different input to that line), is that true? Thank you. -Yuhong ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] preproc-sess -surface flag
Use self for retinotopy doug On 03/26/2013 12:24 PM, Y.V. Jiang wrote: Thanks Doug, this makes sense. What about retinotopic mapping? Should I use fsaverage or self? -Yuhong On Tue, Mar 26, 2013 at 10:56 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: It should either be fsaverage, or self, or an average subject you have created. The fMRI analysis is done such that the raw data are resampled into the fsaverage space (unless you use self) and processed there in anticipation of doing group analysis. doug On 03/26/2013 10:37 AM, Y.V. Jiang wrote: Hi, I wonder if you could help with a basic question for preproc-sess in Version 5.2.0. The flag -surface subject hemi: what should be the entry to subject? The tutorial says fsaverage, but for first-level analysis, should it match subjectname? Or should it always be fsaverage? If it needs to match subjectname, then this command cannot be run in a batch (because different subjects have different input to that line), is that true? Thank you. -Yuhong ___ Freesurfer mailing list 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 gr...@nmr.mgh.harvard.edu mailto:gr...@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: 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@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. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] recon-all bad talairach
Hi Jon, the data are not reoriented or resliced into talairach space. It is just the transform that is computed. To inspect whether this was done right, use tkregister2 --s subject --fstal doug On 03/26/2013 12:20 PM, Jon Wieser wrote: Hello I ran recon-all auto_recon1. and the resulting brainmask file, has a poor talairazation. the ac-pc line is not horizontal, it's tilted, and the interhemisphere fissure is tilted too. how do I fix this? I have attached a picture of the brain ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] R: Re: R: Re: R: Re: R: Re: hippo subfield
Thank you very much Eugenio, you are very kind! Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 26-mar-2013 17.00 A: std...@virgilio.it Cc: zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] R: Re: R: Re: hippo subfield I would say intracranial volume from the aseg.stat table Cheers, /Eugenio On Tue, 2013-03-26 at 16:49 +0100, std...@virgilio.it wrote: Thank you very much Eugenio. I have a last question: Who is the best way to normalize the HippocampalSubfieldSegmentation volume results? Stefano Messaggio originale Da: igles...@nmr.mgh.harvard.edu Data: 26-mar-2013 14.37 A: std...@virgilio.it Cc: zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: R: Re: hippo subfield Ciao, Stefano to compute subfield volumes, you need to use the script kvlQuantifyHippocampalSubfieldSegmentations.sh. The instructions are here: http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation In the wiki page you'll also find instructions to visualize the output. Cheers, /Eugenio On Tue, March 26, 2013 4:40 am, std...@virgilio.it wrote: Hi Zeke and other users, I have finished the Hippocampal Subfields parcellation. New files .mgz are located in $SUBJECTS_DIR/mri. Now, I do not understand as I can calculate for each region the thickness and volume. Can you help me, please? Stefano Messaggio originale Da: zkauf...@nmr.mgh.harvard.edu Data: 23-mar-2013 20.13 A: freesurfer@nmr.mgh.harvard.edufreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] R: Re: hippo subfield It's not enough to simply put the zip file in the /Applications/freesurfer/bin directory,,, you must extract its contents to that directory. Just extract the zip file (anywhere on your machine will do). Then copy and paste the extracted files to /Application/freesurfer/bin -Zeke On Mar 22, 2013, at 7:00 PM, std...@virgilio.it wrote: Hi Zeke, as you explain I have download the kvl.zip and put it in /Application/freesurfer/bin. After rerunning I have: [iMac-di-Stefano:freesurfer/subjects/subject_prova] Stefano% recon-all -s Diff01 -hippo-subfields Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.2.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects/subject_prova Actual FREESURFER_HOME /Applications/freesurfer -rw-rw-r-- 1 Stefano wheel 697785 Mar 22 23:56 /Applications/freesurfer/subjects/subject_prova/Diff01/scripts/recon-all.log Darwin iMac-di-Stefano.local 12.3.0 Darwin Kernel Version 12.3.0: Sun Jan 6 22:37:10 PST 2013; root:xnu-2050.22.13~1/RELEASE_X86_64 x86_64 # #@# Hippocampal Subfields processing Fri Mar 22 23:56:49 CET 2013 \n mkdir -p /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n kvlSegmentHippocampalSubfields.sh Diff01 left /Applications/freesurfer/subjects/subject_prova /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults \n Doing left side meshFileName: /Applications/freesurfer/data/GEMS/CurrentMeshCollection30.gz compressionLookupTableFileName: /Applications/freesurfer/data/GEMS/compressionLookupTable_left.txt boundingBoxFileName: /Applications/freesurfer/data/GEMS/imageDump.mgz subjectName: Diff01 side: left inputDirectory: /Applications/freesurfer/subjects/subject_prova outputDirectory: /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01 already exists directory /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left already exists cd /Applications/freesurfer/subjects/subject_prova/Diff01/tmp/subfieldResults/Diff01/left cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/nu.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/aseg.mgz . cp -f /Applications/freesurfer/subjects/subject_prova/Diff01/mri/transforms/talairach.xfm . cp /Applications/freesurfer/data/GEMS/imageDump.mgz . kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 dyld: Library not loaded: libITKCommon.3.16.dylib Referenced from: /Applications/freesurfer/bin/kvlApplyTransform Reason: image not found /Applications/freesurfer/bin/kvlSegmentHippocampalSubfields.sh: line 18: 5481 Trace/BPT trap: 5 kvlApplyTransform imageDump.mgz -0.9991 -0.0328 0.0258 144.0010 -0.0330 0.9994 -0.0086 2.6560 0.0255 0.0094 0.9996 -3.1939 failed to do kvlApplyTransform imageDump.mgz -0.9991 -0.03280.0258 144.0010 -0.03300.9994 -0.0086
Re: [Freesurfer] Xhemi stat questions
Dear Doug,I meant of a given subject, But, As I'm thinking about this, I'm wondering if it has sense to have left and right cortical thickness of my every individual subjects, or if I should obtain the lh-rh thickness differences for the individuals?I suppose that I should read the lh.lh-rh.thickness.mgh created by mris_preproc to get the average differences in lh-rh hemispheres. Regards,GabrielEl 25/03/13, Douglas N Greve gr...@nmr.mgh.harvard.edu escribió:Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym?dougOn 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer, I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. doug Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values?B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- -- PhD. student Gabriel González-Escamilla Laboratory of Functional Neuroscience Department of Physiology, Anatomy, and Cell Biology University Pablo de Olavide Ctra. de
[Freesurfer] qdec matrix error
Hi list, I'm performing qdec. This my file.dat 1 diagnosis discrete 21 Pathology2 Controls2 Thickness_lh continuous 03 Thickness_rh continuous 04 NPStest continuous 0 Continuous Factors: Mean: StdDev: --- - --- Thickness_lh 2.643 0.116 Thickness_rh 2.630 0.099 NPStest 0.774 1.203 Number of subjects: 31Number of factors:4 (1 discrete, 3 continuous)Number of classes:2Number of regressors: 8 NPStest is scored from 0 to 8. Qdec produces this error: Creating output directory /Applications/freesurfer/subjects/subject_prova/qdec/UntitledLoading y from /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mghINFO: gd2mtx_method is dodsSaving design matrix to /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/Xg.datNormalized matrix condition is 1e+08Design matrix -- 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.712 0.000; 1.000 0.000 0.000 0.000 2.671 0.000; 1.000 0.000 0.000 0.000 2.728 0.000; 1.000 0.000 0.000 0.000 2.646 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.750 0.000; 1.000 0.000 0.000 0.000 2.555 0.000; 1.000 0.000 0.000 0.000 2.784 0.000; 1.000 0.000 0.000 0.000 2.586 0.000; 1.000 0.000 0.000 0.000 2.641 0.000; 1.000 0.000 0.000 0.000 2.561 0.000; 1.000 0.000 0.000 0.000 2.545 0.000; 1.000 0.000 0.000 0.000 2.495 0.000; 1.000 0.000 0.000 0.000 2.769 0.000; 1.000 0.000 0.000 0.000 2.740 0.000; 0.000 1.000 0.000 2.000 0.000 2.526; 0.000 1.000 0.000 2.000 0.000 2.761; 0.000 1.000 0.000 2.000 0.000 2.521; 0.000 1.000 0.000 0.000 0.000 2.592; 0.000 1.000 0.000 2.000 0.000 2.555; 0.000 1.000 0.000 2.000 0.000 2.671; 0.000 1.000 0.000 3.000 0.000 2.559; 0.000 1.000 0.000 3.000 0.000 2.469; 0.000 1.000 0.000 4.000 0.000 2.691; 0.000 1.000 0.000 2.000 0.000 2.522; 0.000 1.000 0.000 0.000 0.000 2.553; 0.000 1.000 0.000 2.000 0.000 2.702; 0.000 1.000 0.000 0.000 0.000 2.738; 0.000 1.000 0.000 0.000 0.000 2.789; 0.000 1.000 0.000 0.000 0.000 2.651;ERROR: matrix is ill-conditioned or badly scaled, condno = 1e+08Possible problem with experimental design:Check for duplicate entries and/or lack of range ofcontinuous variables within a class.If you seek help with this problem, make sure to send: 1. Your command line:mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat 2. The FSGD file (if using one) 3. And the design matrix aboveError in Analyze: command failed: mri_glmfit --y /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/y.mgh --fsgd /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/qdec.fsgd dods --glmdir /Applications/freesurfer/subjects/subject_prova/qdec/Untitled --surf fsaverage lh --label /Applications/freesurfer/subjects/subject_prova/fsaverage/label/lh.aparc.label --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Avg-thickness-NPStest-Cor.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Intercept-thickness.mat --C /Applications/freesurfer/subjects/subject_prova/qdec/Untitled/contrasts/lh-Diff-Controls-Pathology-Cor-thickness-NPStest.mat I don't understand what's happen? Thanks, Stefano ___ 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
[Freesurfer] Admin please unsubscribe this email!
Admin please unsubscribe this email address Thanks, Manish Dalwani ___ 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] Fwd: Brodmann area thickness, surface area and volume
After running the mri_label2label and mris_label2annot a new rh.BA.annot file was created (I had to remove the old one since it doesn't overwritte) but when running [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white It says that can't read annotation file: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//SUBJECT/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory I only tried with rh, but I don't think that's a problem is it? Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: In the BA label section there are: - Several mri_label2label commands that map each label from fsaverage space to your indidvidual's space - One mris_label2annot command that combines the mapped label into an annotation file. - One mris_anatomical_stats command that gets stats for that annotation. For each of these commands you can run them with --help to see what the inputs and outputs are, or look them up on the wiki. On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: Nevermind the last email... If I change the output (wich is the second place where BAxx.label appears, right?) file name and give the subjs id this won't be a problem... Anyway, what are these files for? Will I need to use them somehow? Thanks Andreia Quoting _andre...@sapo.pt: Addicionaly, this approach is creating an individual file for each BAxxx.thresh.label (see atchment) and I think that if I run these commands for another subject these outputs will be replaced since the name of the files has no info relating to the subject who it belongs. I'm kind of lost here... Quoting _andre...@sapo.pt: Hi, I run the command for each BA labels of the right hemisphere and then run: [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white Which resulted in: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory What is wrong? Is there a way to run everything that is needed to get the BA stats at once using the BAxxx.thresh.label? Thank you, Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output. Run *all* the commands from the BA labels section, all the way to the end of that section, this will get you to the stats. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold? Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label --trgsubject SUSANAFERREIRA --trglabel ./rh.BA1.label --hemi rh --regmethod surface And I tried substituing BAxxx.label by BAxxx.thresh.label like this: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/lh.BA1.threshold.label --trgsubject SUSANAFERREIRA --trglabel ./lh.BA1.thresolh.label --hemi lh --regmethod surface gave an error : SUBJECTS_DIR /home/user/visao/Freesurfer/ FREESURFER_HOME /usr/local/freesurfer Loading source label. No such file or
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
What's the location of the new rh.BA.annot that was created by mris_label2annot? You need to pass that same file to mris_anatomical_stats with the -a option. On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: After running the mri_label2label and mris_label2annot a new rh.BA.annot file was created (I had to remove the old one since it doesn't overwritte) but when running [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white It says that can't read annotation file: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//SUBJECT/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory I only tried with rh, but I don't think that's a problem is it? Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: In the BA label section there are: - Several mri_label2label commands that map each label from fsaverage space to your indidvidual's space - One mris_label2annot command that combines the mapped label into an annotation file. - One mris_anatomical_stats command that gets stats for that annotation. For each of these commands you can run them with --help to see what the inputs and outputs are, or look them up on the wiki. On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: Nevermind the last email... If I change the output (wich is the second place where BAxx.label appears, right?) file name and give the subjs id this won't be a problem... Anyway, what are these files for? Will I need to use them somehow? Thanks Andreia Quoting _andre...@sapo.pt: Addicionaly, this approach is creating an individual file for each BAxxx.thresh.label (see atchment) and I think that if I run these commands for another subject these outputs will be replaced since the name of the files has no info relating to the subject who it belongs. I'm kind of lost here... Quoting _andre...@sapo.pt: Hi, I run the command for each BA labels of the right hemisphere and then run: [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white Which resulted in: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory What is wrong? Is there a way to run everything that is needed to get the BA stats at once using the BAxxx.thresh.label? Thank you, Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output. Run *all* the commands from the BA labels section, all the way to the end of that section, this will get you to the stats. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold? Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's .thresh.label, not .threshold.label. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Hi Anastasia! The command in the recon-all.log is this one: mri_label2label --srcsubject fsaverage --srclabel /home/user/visao/Freesurfer/fsaverage/label/rh.BA1.label
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
It was automatically created in the same folder of the old one - label However, inside this folder there are the old rh.BAxxx.label. The new ones (BAxxx.thresh.label) were created inside the Freesurfer folder, could it be related to that? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What's the location of the new rh.BA.annot that was created by mris_label2annot? You need to pass that same file to mris_anatomical_stats with the -a option. On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: After running the mri_label2label and mris_label2annot a new rh.BA.annot file was created (I had to remove the old one since it doesn't overwritte) but when running [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white It says that can't read annotation file: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//SUBJECT/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//SUBJECT/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory I only tried with rh, but I don't think that's a problem is it? Thank you! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: In the BA label section there are: - Several mri_label2label commands that map each label from fsaverage space to your indidvidual's space - One mris_label2annot command that combines the mapped label into an annotation file. - One mris_anatomical_stats command that gets stats for that annotation. For each of these commands you can run them with --help to see what the inputs and outputs are, or look them up on the wiki. On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: Nevermind the last email... If I change the output (wich is the second place where BAxx.label appears, right?) file name and give the subjs id this won't be a problem... Anyway, what are these files for? Will I need to use them somehow? Thanks Andreia Quoting _andre...@sapo.pt: Addicionaly, this approach is creating an individual file for each BAxxx.thresh.label (see atchment) and I think that if I run these commands for another subject these outputs will be replaced since the name of the files has no info relating to the subject who it belongs. I'm kind of lost here... Quoting _andre...@sapo.pt: Hi, I run the command for each BA labels of the right hemisphere and thenrun: [user@host87 Freesurfer]$ mris_anatomical_stats -mgz -f ../stats/rh.BA.thresh.stats -b -a ./rh.BA.annot -c ./BA.ctab SUBJECT rh white Which resulted in: INFO: assuming MGZ format for volumes. computing statistics for each annotation in ./rh.BA.annot. reading volume /home/user/visao/Freesurfer//ANTONIOVELOSO_2/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... reading input pial surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.pial... reading input white surface /home/user/visao/Freesurfer//ANTONIOVELOSO_2/surf/rh.white... could not read annot file ./rh.BA.annot No such file or directory mris_anatomical_stats: could not read annotation file ./rh.BA.annot No such file or directory What is wrong? Is there a way to run everything that is needed to get the BA stats at once using the BAxxx.thresh.label? Thank you, Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: If you replace *every* occurence of BAxxx.label with BAxxx.thresh.label, this will keep things simple and you won't have to worry about which one is input and which one is output. Run *all* the commands from the BA labels section, all the way to the end of that section, this will get you to the stats. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ok. So the first is the input and the second is the output, correct? So I'll have a different file for each out put? Is it possible to have a table with the different measures after the threshold? Thank you very much and I apologize for the naive questions... Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: What you call the output label is up to you. What you call the input label is more important - it has to be a file that actually exists. On Mon, 25 Mar 2013, _andre...@sapo.pt wrote: Ah ok! Sorry... In both places? Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: It's
Re: [Freesurfer] Xhemi stat questions
Unless you specifically need them for an individual, you should get them from lh.lh-rh.thickness.mgh because that data is sampled onto the symmetric template and so should be unbiased (ie, it will not systematically favor lh or rh). doug On 03/26/2013 12:40 PM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I meant of a given subject, But, As I'm thinking about this, I'm wondering if it has sense to have left and right cortical thickness of my every individual subjects, or if I should obtain the lh-rh thickness differences for the individuals? I suppose that I should read the lh.lh-rh.thickness.mgh created by mris_preproc to get the average differences in lh-rh hemispheres. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: Do you mean you want the right hemi thicknesses on the left hemisphere of a given subject or on the fsaverage_sym? doug On 03/25/2013 11:25 AM, Gabriel Gonzalez Escamilla wrote: Thank you, so I'm keeping the one I had. Sorry for my bad explanation. When I do a normal cortical thickness study, I know the average thickness for a label, e.g. cortex, and the values at each vertex of each hemisphere are stored in $subject/surf/?l.thickness. I would like to know if it is possible to obtain the same cortical thickness measure from the lh-rh registered hemispheres of each subject. Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/25/2013 10:52 AM, Gabriel Gonzalez Escamilla wrote: Thanks a lot for your answer, I'm sending you attached the diff of the two mris_preproc. Those differences are just added features and won't change your results. When I wrote CT, I was meaning cortical thickness, as normally this values are in surf/?h.thickness, But how do I know the Xhemi-registered thickness values of each subject for lh-rh, or area or any of those indices? I'm not sure what you mean. When you run mris_preproc, you specify whether you want thickness, etc. doug Regards, Gabriel El 25/03/13, *Douglas N Greve * gr...@nmr.mgh.harvard.edu escribió: On 03/22/2013 06:45 AM, Gabriel Gonzalez Escamilla wrote: Dear Doug, I've seen that you restore the files to download, for the Xhemi registration. While I'm checking for the statistical process, I've seen that the one I have is: Date: 2012/12/06 16:06:52, Revision: 1.59.2.4, and the one that is on your ftp server is Date: 2012/12/06 16:06:17, Revision: 1.66, So mine is a lower version but recent hour, and the actual is newer version but seems that was created before the one I have. My question is, Which one should I keep? Can you send me a diff of the two files? If I change the mris_precproc version. Shall I re-run this step before statistical analyses, to create a new lh.lh-rh.thickness.sm00.mgh? On the other hand I have some doubts about the statistical procedure. It's supposed that if I apply the Xhemi registration, as result the left and right hemispheres are equals to each other on every subject, so: A) Where can I get the CT values after the Xhemi registration to FSaverage_sym for the left and right hemispheres? what are CT values? B) Given that I have two groups, Patients and Control, with two levels each, i.e male-female (Gp1male Gp1female Gp2male Gp2female Gp1maleVar1 Gp1femaleVar1 Grp2maleVar1 Grp2femaleVar1), and that I can set the contrasts and fsgd files as with a normal CT analisis, but only on my lh.lh-rh.thickness.smXX.mgh, wich is suppose to contain the left-right differences across subjects, right? Wich would be the right interpretation? of: The interpretation does not really change because it is a xhemi analysis 1) 5 .5 -.5 -.5 0 0 0 0 Is the L-R difference between Grp1 and Grp2 different than 0 (regressing out Var1 and gender) 2) 5 -.5 .5 -.5 0 0 0 0 Is the L-R difference between Males and Females different than 0 (regressing out Var1 and Group) 3) 0 0 0 0 .5 .5 -.5 -.5 Does the slope of the L-R difference with Var1 differ between Grp1 and Grp2(regressing out gender) 4) 0 0 0 0 5 -.5 .5 -.5 Does the slope of the L-R difference with Var1 differ between Male and Female(regressing out group) Many thanks in advanced. Gabriel. -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for
Re: [Freesurfer] recon-all bad talairach
Hi Jon, it is not supposed to be horizontal. The anatomy in the target is just supposed to match that in the moveable. doug ps. please respond to the list. thanks! On 03/26/2013 02:35 PM, Jon Wieser wrote: HI doug, i viewed it with tkregister2. the transform looks poor, the ac-pc line is not horizontal. i have attached a pic Jon - Original Message - From: Douglas N Greve gr...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, March 26, 2013 11:28:01 AM Subject: Re: [Freesurfer] recon-all bad talairach Hi Jon, the data are not reoriented or resliced into talairach space. It is just the transform that is computed. To inspect whether this was done right, use tkregister2 --s subject --fstal doug On 03/26/2013 12:20 PM, Jon Wieser wrote: Hello I ran recon-all auto_recon1. and the resulting brainmask file, has a poor talairazation. the ac-pc line is not horizontal, it's tilted, and the interhemisphere fissure is tilted too. how do I fix this? I have attached a picture of the brain ___ 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Fwd: Brodmann area thickness, surface area and volume
No problem, you can usually find the answers to most of these types of questions in the help text of the commands. For example if you run mris_label2annot --help you'll see: [...] --a annotname Name of the annotation to create. The actual file will be called hemi.annotname.annot, and it will be created in subject/label. If this file exists, then mris_label2annot exits immediately with an error message. It is then up to the user to manually delete this file (this is so annotations are not accidentally deleted, which could be a huge inconvenience). [...] On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: Oh so that was it... I've cd to the dir where the annot file is and now everything worked just fine... I checked the values in the stats file and they are smaller now. So I must do that when running the label2label so the files are created in the label dir and not in Freesurfer dir... By the way, why did the command label2annot created the file in the right dir? As you're noticing I'm not very familiar with Unix and while using Freesurfer I never had to use the cd command to work... Thank you very much Anastasia! ___ 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] subcortical segmentation
A subcortical segmentation error sometimes get Freesurfer (v 5.1) is cortical areas coming over into the hippocampus, ignoring the wm inferior and lateral to the hippocmapus (coronal). See attached png. Will adding wm control points help, or do they not inform the aseg segmentation. What is the best way to (non-manually) fix this kind of issue? - Josh attachment: s.png___ 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] Fwd: Brodmann area thickness, surface area and volume
I'll bear that in mind next time! Thank you!! Andreia Quoting Anastasia Yendiki ayend...@nmr.mgh.harvard.edu: No problem, you can usually find the answers to most of these types of questions in the help text of the commands. For example if you run mris_label2annot --help you'll see: [...] --a annotname Name of the annotation to create. The actual file will be called hemi.annotname.annot, and it will be created in subject/label. If this file exists, then mris_label2annot exits immediately with an error message. It is then up to the user to manually delete this file (this is so annotations are not accidentally deleted, which could be a huge inconvenience). [...] On Tue, 26 Mar 2013, _andre...@sapo.pt wrote: Oh so that was it... I've cd to the dir where the annot file is and now everything worked just fine... I checked the values in the stats file and they are smaller now. So I must do that when running the label2label so the files are created in the label dir and not in Freesurfer dir... By the way, why did the command label2annot created the file in the right dir? As you're noticing I'm not very familiar with Unix and while using Freesurfer I never had to use the cd command to work... Thank you very much Anastasia! 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] view retinotopy results in version 5
Hi, I was able to view retinotopic mapping results using rtview in version 5. However, the display was on the inflated surface. Is there a way to view the results on the flattened occipital map, similar to version 4's surf-sess -flat? Thanks! -Yuhong ___ 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] subcortical segmentation
Hi Josh it might if the white matter is very dim, as it appears in your images. You might also try 5.2, which I think is better about this kind of thing. If you try control points, make sure that they get applied in the mri_ca_normalize step and not just to cortical normalizaation in mri_normlaize (in some versions they were applied to both, but that made people unhappy so we backed off on it) cheers Bruce On Tue, 26 Mar 2013, Joshua Lee wrote: A subcortical segmentation error sometimes get Freesurfer (v 5.1) is cortical areas coming over into the hippocampus, ignoring the wm inferior and lateral to the hippocmapus (coronal). See attached png. Will adding wm control points help, or do they not inform the aseg segmentation. What is the best way to (non-manually) fix this kind of issue? - Josh ___ 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] memory allocation errors on Snow Leopard running dmri_train
Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz
[Freesurfer] More QDEC questions
Hi everyone, My QDEC analysis ran into an error message that seems to be a classic (and, so far, it seems unsolved), from mri_concat, which I've described in a separate message, just sent. I have, however, more theoretical questions about QDEC, which I hope some kind soul will help me with: - why does QDEC only provide the volume of *subcortical* structures under StatsDataImport/aseg.volume, when the automatic GM/WM segmentation is done for the entire brain, not just for subcortical regions? - how are the volume measurements provided in aseg.volume different from the ones done obtained with a VBM analysis? - why is *volume *the result of *segmentation *(aseg.volume) whereas *thickness *derives from *parcelation *(rh.aparc.thickness)? Is it not the case that both operations (segmentation+parcellation) are necessary to calculate volume as well as thickness? - how is a QDEC thickness analysis different from a regular AN(C)OVA in which you are interested in main and interaction effects of the IVs on the DV? I ask this because some of the questions that appear in QDEC's Analysis Results tab – e.g. is the correlation between (DV) and (IV) different from zero? – would not (I think) be directly answerable by an ANOVA - would the same type of ANOVA done by QDEC be doable by extracting the values of the DV for each subject (using e.g. *aseg.volume*) and then doing the ANOVA in e.g. SPSS? If so, when would you do one versus the other? - why is it that only continuous factors (e.g. age) can be taken in the analysis as nuisance factors, when discrete variables (e.g. gender) might also be irrelevant for a particular analysis and thus belong to the Nuisance Factor list? Many thanks in advance!! Tudor ___ 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] memory allocation errors on Snow Leopard running dmri_train
Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz
[Freesurfer] trackstats2table error
I am trying to convert my dti tracts stats to a table and got the following error tractstats2table --inputs fmajor_PP_avg23_mni_flt/pathstats.overall.txt --overall --tablefile table.txt Traceback (most recent call last): File /usr/local/freesurfer/bin/tractstats2table, line 9, in module from fsutils import TractOverallStatsParser, TractByvoxelStatsParser, BadFileError, tractlogger ImportError: cannot import name TractOverallStatsParser -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ 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] memory allocation errors on Snow Leopard running dmri_train
Hi Anastasia, It had the same issue before, but worked fine after installing the fixed dmri patch for Snow Leopard. Thanks. ping On Tue, Mar 26, 2013 at 5:09 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Ping - Are you running this on the same system where you were running the 5.1 snow leopard build without a problem? a.y On Tue, 26 Mar 2013, Ping-Hong Yeh wrote: Hi FS users, I've tested the newer Tracula FS 5.2 on Snow Leopard and ran into errors. The 5.2 recon-all of T1 was finished ok. Here is the final part of log file. #@# Priors Tue Mar 26 14:39:36 EDT 2013 /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz dlabel/mni/rh.cst_AS_roi2.flt.nii.gz dlabel/mni/lh.ilf_AS_roi1.flt.nii.gz dlabel/mni/lh.ilf_AS_roi2.flt.nii.gz dlabel/mni/rh.ilf_AS_roi1.flt.nii.gz dlabel/mni/rh.ilf_AS_roi2.flt.nii.gz dlabel/mni/lh.unc_AS_roi1.flt.nii.gz dlabel/mni/lh.unc_AS_roi2.flt.nii.gz dlabel/mni/rh.unc_AS_roi1.flt.nii.gz dlabel/mni/rh.unc_AS_roi2.flt.nii.gz dlabel/mni/fmajor_PP_roi1.flt.nii.gz dlabel/mni/fmajor_PP_roi2.flt.nii.gz dlabel/mni/fminor_PP_roi1.flt.nii.gz dlabel/mni/fminor_PP_roi2.flt.nii.gz dlabel/mni/lh.atr_PP_roi1.flt.nii.gz dlabel/mni/lh.atr_PP_roi2.flt.nii.gz dlabel/mni/rh.atr_PP_roi1.flt.nii.gz dlabel/mni/rh.atr_PP_roi2.flt.nii.gz dlabel/mni/lh.cab_PP_roi1.flt.nii.gz dlabel/mni/lh.cab_PP_roi2.flt.nii.gz dlabel/mni/rh.cab_PP_roi1.flt.nii.gz dlabel/mni/rh.cab_PP_roi2.flt.nii.gz dlabel/mni/lh.ccg_PP_roi1.flt.nii.gz dlabel/mni/lh.ccg_PP_roi2.flt.nii.gz dlabel/mni/rh.ccg_PP_roi1.flt.nii.gz dlabel/mni/rh.ccg_PP_roi2.flt.nii.gz dlabel/mni/lh.slfp_PP_roi1.flt.nii.gz dlabel/mni/lh.slfp_PP_roi2.flt.nii.gz dlabel/mni/rh.slfp_PP_roi1.flt.nii.gz dlabel/mni/rh.slfp_PP_roi2.flt.nii.gz dlabel/mni/lh.slft_PP_roi1.flt.nii.gz dlabel/mni/lh.slft_PP_roi2.flt.nii.gz dlabel/mni/rh.slft_PP_roi1.flt.nii.gz dlabel/mni/rh.slft_PP_roi2.flt.nii.gz --bmask /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni/aparc+aseg_mask.nii.gz --fa /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/dtifit_FA.nii.gz --cptdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/diff --reg /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dmri/xfms/mni2diff.flt.mat --ncpts 10 --trunc cwd /Users/twbrkmp2 cmdline /apps/freesurfer/bin/dmri_train --outdir /Volumes/Access_Point_Backup/freesurfer/NCNC2348/dlabel/mni --out lh.cst_AS_avg33_mni_flt rh.cst_AS_avg33_mni_flt lh.ilf_AS_avg33_mni_flt rh.ilf_AS_avg33_mni_flt lh.unc_AS_avg33_mni_flt rh.unc_AS_avg33_mni_flt fmajor_PP_avg33_mni_flt fminor_PP_avg33_mni_flt lh.atr_PP_avg33_mni_flt rh.atr_PP_avg33_mni_flt lh.cab_PP_avg33_mni_flt rh.cab_PP_avg33_mni_flt lh.ccg_PP_avg33_mni_flt rh.ccg_PP_avg33_mni_flt lh.slfp_PP_avg33_mni_flt rh.slfp_PP_avg33_mni_flt lh.slft_PP_avg33_mni_flt rh.slft_PP_avg33_mni_flt --slist /tmp/subj33.NCNC2348.61836.txt --trk dlabel/mni/lh.cst_AS.flt.trk dlabel/mni/rh.cst_AS.flt.trk dlabel/mni/lh.ilf_AS.flt.trk dlabel/mni/rh.ilf_AS.flt.trk dlabel/mni/lh.unc_AS.flt.trk dlabel/mni/rh.unc_AS.flt.trk dlabel/mni/fmajor_PP.flt.trk dlabel/mni/fminor_PP.flt.trk dlabel/mni/lh.atr_PP.flt.trk dlabel/mni/rh.atr_PP.flt.trk dlabel/mni/lh.cab_PP.flt.trk dlabel/mni/rh.cab_PP.flt.trk dlabel/mni/lh.ccg_PP.flt.trk dlabel/mni/rh.ccg_PP.flt.trk dlabel/mni/lh.slfp_PP.flt.trk dlabel/mni/rh.slfp_PP.flt.trk dlabel/mni/lh.slft_PP.flt.trk dlabel/mni/rh.slft_PP.flt.trk --seg dlabel/mni/aparc+aseg.nii.gz --cmask dlabel/mni/cortex+2mm.nii.gz --lmask 16 16 0 0 0 0 0 0 10 49 0 0 0 0 0 0 0 0 --rois dlabel/mni/lh.cst_AS_roi1.flt.nii.gz dlabel/mni/lh.cst_AS_roi2.flt.nii.gz dlabel/mni/rh.cst_AS_roi1.flt.nii.gz
[Freesurfer] sort labels by lobes
Dear all, I have a brain segmented with Freesurfer 2009 and a list with label description looking like this: ... 11101 ctx_lh_G_and_S_frontomargin 12101 ctx_rh_G_and_S_frontomargin 11102 ctx_lh_G_and_S_occipital_inf 12102 ctx_rh_G_and_S_occipital_inf ... What is the best way to sort labels by lobes based on the name or the number? Are there any publications with this information or a table somewhere on Freesurfer web-page? Sincerely yours, Anna Varentsova ___ 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] trackstats2table error
i fixed the problem - Original Message - From: Jon Wieser wie...@uwm.edu To: freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Tuesday, March 26, 2013 4:21:35 PM Subject: [Freesurfer] trackstats2table error I am trying to convert my dti tracts stats to a table and got the following error tractstats2table --inputs fmajor_PP_avg23_mni_flt/pathstats.overall.txt --overall --tablefile table.txt Traceback (most recent call last): File /usr/local/freesurfer/bin/tractstats2table, line 9, in module from fsutils import TractOverallStatsParser, TractByvoxelStatsParser, BadFileError, tractlogger ImportError: cannot import name TractOverallStatsParser -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ 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. -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219 ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Error in Talairach transform version 5.2
I'm having some recon-all errors like this: mritotal -verbose -debug -clobber -modeldir /usr/local/freesurfer/mni/bin/../share/mni_autoreg -protocol icbm transforms/tmp.talairach.3505/src.mnc transforms/talairach.auto.xfm Use of uninitialized value $path in join or string at /usr/local/freesurfer/mni/bin/mritotal line 462. mritotal: Couldn't find configuration file mritotal.cfg anywhere in :/usr/local/freesurfer/mni/bin/../etc/mni_autoreg ERROR: mritotal failed, see transforms/talairach.log Linux ip-10-147-137-177 3.2.39-6.88.amzn1.i686 #1 SMP Sat Mar 2 05:13:38 UTC 2013 i686 i686 i386 GNU/Linux recon-all -s caso765 exited with ERRORS at Mon Mar 25 19:24:29 UTC 2013 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Is this file /usr/local/freesurfer/mni/bin/../etc/mni_autoreg really missing in the distribution? ___ 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] surf2vol
Does leftfrontallobe.nii.gz overlay properly in tkmedit? eg, tkmedit subject orig.mgz -surfs -overlay leftfrontallobe.nii.gz -fminmax .5 1 doug On 03/26/2013 07:20 AM, Daniel Lumsden wrote: Bruce Many thanks - that's given me a lot more guidance. Following the help, i've put together the command below: mri_surf2vol --hemi lh --template path to/orig.mgz --outvol path to where I want the file/leftfrontallobe.nii.gz --surfval path to/left_frontal_lobe.gii --fillribbon --volregidentity mov07 Where mov07 is my subjid and left_frontal_lobe.gii is the surface I've generated from the label files to run in probtrakx. This command runs, but produces and empty nifti file. I've changed the output to .mgz with similar effect. I've substituted the rawavg.mgz file for the orig.mgz file, and tried both .nii.gz and .mgz versions of both files and still get an empty output file. The subject is in my $SUBJECTS_DIR. Is there a way to check the .gii files? I generated them using label2surf, having used mris_convert to convert the lh.white and rh.white files from the surf folder for my subject to lh.white.asc and rh.white.asc. Thank you again for your help. Dan Date: Mon, 25 Mar 2013 14:59:28 -0400 From: fis...@nmr.mgh.harvard.edu To: doclums...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] surf2vol Hi Dan try using mri_surf2vol instead (it has a much bigger help, thanks to Doug0 Bruce On Mon, 25 Mar 2013, Daniel Lumsden wrote: Dear All Apologies for what I'm sure is a very basic question. I'm new to using freesurfer, and would like to generate cortical parcellations for running in probtrakx. I have followed the instructions from various sources and have managed to generate the parcellations from recon-all, extract the label files from the parcellation, then use mri_mergelabels and label2surf to generate the the .gii files needed for probtrakx. I'd like to be able to display the surface files for illustrative purposes, but I'm struggling to apply the surf2vol command. From the terminal window I can see that the commands required are: surf2vol surf refvol outvol convention I presume that surf is the .gii file I'm trying to visualise, and outvol is to specify the name of the output volume the command will generate, but what should I be using as the refvol? I would be very grateful for any guidance. Please accept my apologies if I've missed a very obvious online explanation for this and thank you in advance. Dan Lumsden Clinical Research Fellow 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 -- 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 Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] License invalid after upgrading OS (opensuse) - still not working
Hi List, with reference to my below messages, I have now determined that the license file is considered invalid by freesurfer executables since i have upgraded from opensuse 12.2 to 12.3. The upgrade to freesurfer 5.2 had nothing to do with it - in fact, setting the proper environments variables and running 5.1 from by backed up, untouched, old install dir and .license file changes nothing (i.e. not even 5.1 is working now). Any idea what my be going on here? I have tried every combination of file permissions and contents I could think of. Much appreciated Nicola On 3/22/2013 5:36 PM, Nicola Toschi wrote: Hi, that is exactly what I did (see my first message) - that's why I'm so puzzled! Nicola On 03/22/2013 05:05 PM, Lingqiang Kong wrote: Just use the license file from your previous version (or you can apply for a new license for free, but this is redundant). cp $OLD_FREESURFER_HOME/.license $NEW_FREESURFER_HOME/.license where the $OLD and $NEW are directories freesurfer 5.1 and 5.2 sit, respectively. Lingqiang Hi - no luck unfortunately (I had already tried changing permissions) On 03/22/2013 04:09 PM, Varghese Chikku wrote: Hi Nicola, Can you try this command,and echo the license.It may ask for password.I have similar issues with 5.2 and this how i sorted. sudo chmod -R a+rwX /Applications/freesurfer then echo each line of the licence. Let me know In thanks chikku ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Merging PArcellation labels
Hi Anupa, In addition to the Desikan and Destrieux parcellations, FreeSurfer 5.2 also include other cortical parcellations (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes). In particular, the resting-state parcellation or Mindboggle atlas might be relevant to you if you are interested in the frontal cortex. Cheers, Thomas On Mon, Mar 25, 2013 at 11:31 PM, Laura M. Tully tully.la...@googlemail.com wrote: it sounds like you want a different parcellation of the lateral prefrontal cortex than what is offered by the default atlas (aparc, AKA the desikan atlas) - I suggest you load in ?h.aparc.a2009s.annot (aka the destrieux atlas) as your annotation in tksurfer and select the annotations of the PFC that you want from there and save as labels. The aparc.a2009 annotation offers a more fine grained parcellation of the PFC - e.g. you can get the DLPFC by merging the middle frontal gyrus middle frontal sulcus parcellations. On Mon, Mar 25, 2013 at 3:19 AM, Anupa AV av.an...@yahoo.com wrote: Dear Laura, Thank you so much. It worked well. Do you know how to make cuts on the merged label, for eg. if I need to seperate DLPFC from premotor cortex. From: Laura M. Tully tully.la...@googlemail.com To: Anupa AV av.an...@yahoo.com Cc: freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu Sent: Sunday, March 24, 2013 12:20 AM Subject: Re: [Freesurfer] Merging PArcellation labels First save each parcellation that you want as its own separate label by selecting it in tksurfer (simply click on it with your mouse and its boarder will be highlighted in yellow) and then file - label - save selected label... Then you can merge these separate labels into one label at the command line using mri_mergelabels -i [labelfile1] -i [labelfile2] -o [newlabelfile.label] If doing glms from the command line you can then feed mri_glmfit the label with the --label option. This will conduct the glm in the region specified in the label only (i.e. an roi analysis) There is also a quick way to turn all of the desikan parcellations into individual label files at the command line using mri_annotation2label I think, but I can't remember precisely. This is a lot faster than using tksurfer as it simply dumps all the individual parcellations into a specified output directory. But I don't know if you can do it with the Destrieux atlas parcellations (if you were interested in doing that.) Laura. On Sat, Mar 23, 2013 at 2:36 AM, Anupa AV av.an...@yahoo.com wrote: Dear All, Can anyone tell me how to merge the parcellation labels using tksurfer.? For eg. How can I merge, Superior frontal gyrus, middle frontal gyrus and caudal middle frontal gyrus. ___ 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. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ 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. -- -- Laura M. Tully, MA Social Neuroscience Psychopathology, Harvard University Center for the Assessment and Prevention of Prodromal States, UCLA Semel Institute of Neuroscience ltu...@mednet.ucla.edu ltu...@fas.harvard.edu 310-267-0170 -- My musings as a young clinical scientist: http://theclinicalbrain.blogspot.com/ Follow me on Twitter: @tully_laura ___ 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
[Freesurfer] getting started with ROI labels
Dear Freesurfers, I'm interested in using FS identified labels, such as Brodman areas in the anatomical volume, to measure a feature, say mean intensity in V1, in a second volume registered to the first. I'm new to the use of labels, so some advice on where to start would be appreciated. Thanks, Fred Lado, MD PhD Director, Neurology Service - Moses North Divisions Director, EEG Laboratory Associate Clinical Professor of Neurology Montefiore Medical Center 718-920-8499 office 718-324-3730 fax email: fl...@montefiore.org Confidentiality Notice: This document is protected by EDUCATIONAL LAW 6527 PUBLIC HEALTH LAW 2085, J, K, L, M. This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited and may be unlawful. If you are not the intended recipient, please delete this e-mail immediately. ___ 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] Incomplete and poorly formed tracts
Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH 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/**compliancelinehttp://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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle,* Sherlock Holmes- Valley of Fear* ___ 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 get surface-based AAL template
Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes.___ 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] How to get surface-based AAL template
Hi, In my case transformation to fsaverage did not work very well. What I did was: - from Surfrend page download Colin 27 subject and transform it to the latest version (now 5.2) - with bbregister obtain register.dat between this Colin 27 subject and SPM-s single subject t1.nii, which is the 2mm version of Colin 27. AAL-s are defined in Colin 27. As they are the same subject, the registering is very good. - now you can import every AAL ROI (in .nii form) to an annotation or in the form of individual labels to your FS Colin 27, using the newly created registering file. - now you can use surf2surf or label2label to go to your subjects and obtain stats. Br! On 27/03/2013, at 05:35, ZhiLiangLong lagosslong1...@163.com wrote: Hi all; I need a suface-based aal template which is compatible with FS surface file. Is there a way i can get the surface-based aal template? I have an idea, that is to just transform the AAL template (.nii file) in MNI space onto the surface template (e.g. fsaverage template) in FS. Is it correct? if in this case, how can i do the transformation? Any suggestions appreciated. Besh wishes. ___ 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] Incomplete and poorly formed tracts
Hi Susie - Everything under dlabel/diff is mapped to DWI space (either with flirt or with bbregister, whichever you use). The one in my screenshot was dlabel/diff/aparc+aseg.flt.nii.gz. a.y On Wed, 27 Mar 2013, Susan Kuo wrote: Hi Anastasia, I see what you mean. I had previously used the dtifit_FA.nii.gz image and overlaid that with the aparc+aseg+2mm.nii.gz image in /dlabel/diff, using freeview. I didn't end up with the same images as you, however. Can you tell me which images you used to obtain this overlay? I am going to run bbregister tonight, and I'll let you know how it goes -- I'm hopeful! Thank you again! Susie Kuo NIH On Tue, Mar 26, 2013 at 5:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susie - I'm attaching a snapshot from your subject, showing the aparc+aseg overlaid on the FA map. The registration has failed. The frontal lobe has spilled out of the brain, the white matter has spilled into the ventricles. I strongly recommend using bbregister for the intra-subject registration, which is the default in the latest version of trac-all. Hope this helps, a.y On Tue, 26 Mar 2013, Susan Kuo wrote: Hi Anastasia, I did as you recommended and checked the diffusion-to-anatomical registration, and the overlay of aparc+aseg_mask on FA, and these views seem to be good. Upon closer inspection, what I find is that there are incipient 'bits' of all the tracts, but they seem to not have 'grown', though they are in the proper space (comparing them to good brains that yielded the full complement of tracts). Is there a configuration in your TRACULA that controls the growing of the tracts specifically? Perhaps I should look into that. Thank you, btw, for your very prompt reply yesterday- it was much appreciated! Sincerely, Susie Kuo NIH On Mon, Mar 25, 2013 at 4:58 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Susan - Good to hear that you get good results for most of your subjects. Have you checked the aparc+aseg and the diffusion-to-anatomical registration for the subjects that are failing? I'd check the aparc+aseg_mask (in the dlabel/diff directory) over the FA map to see if there are any holes or misregistration. a.y On Mon, 25 Mar 2013, Susan Kuo wrote: Hi FreeSurfers and Anastasia, TRACULA is working great for me, generating tracts for a sample of 20 subject brains I'm working with. However, for 3 of the brains, I'm receiving incomplete and poorly formed tracts. I've re-run trac-all at least 2x on each subject in case there was a mistake in my original configuration. However, I am reproducing the same results. Does anybody have an idea why I would see these spotty tracts? Thank you for all your help! -- Susie Kuo NIH 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. -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear -- Susie Kuo Mediocrity knows nothing higher than itself, but talent instantly recognizes genius. - Sir Arthur Conan Doyle, Sherlock Holmes- Valley of Fear ___ 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
