[Freesurfer] WM of lobes
Dear freesurfersI'm trying to get the WM parcellation by lobes, I have read some previous FS archives regarding a similar topic, but they only want the volume value, and I'm interested in a WM lobes parcellation in mgz format (like aseg.mgz ), and I'm also interested in knowing if is possible to obtain this lobar parcellation for only cortical WM. Many thanks in advanced,Gabriel ___ 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] nu_correct problem (fwd)
Please remember to cc the list. -- Forwarded message -- Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET) From: zach.p...@post.cz To: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Subject: Re: Re: [Freesurfer] nu_correct problem Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web page (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi, Documentation) I´ll send recon-all.log file later on I have it on another PC. Orig.mgz file - thats also problem. What I did: when running recon-all -subjid name -autorecon1 I get error: no /mri/orig/orig.mgz file. I looked into patients /mri directory and this path and file is not there. So that I created directory /orig in /mri and copied there converted patient.mgz file there and renamed it to orig.mgz. So that I have /subject/patient/mri/orig/orig.mgz. Maybe thats what is wrong? How do you get normally orig.mgz file? Thanks, Petr -- Původní zpráva -- Od: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Datum: 16. 1. 2013 Předmět: Re: [Freesurfer] nu_correct problem Hi Petr, Can you provide us with some more details? Which version of FreeSurfer are you using and on what platform? Could you attach a copy of the recon-all.log file for one of these cases so we can read the full error reported? Have you tried looking at the orig.mgz which is generated prior to the mri_nu_correct.mni step to see if it looks reasonable? -Louis On Wed, 16 Jan 2013, zach.p...@post.cz wrote: Dear members, when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu_correct. This happens for DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? Thanks much, Petr Zach 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] nu_correct problem (fwd)
Hi Petr, Try renaming /subject/patient/mri/orig/orig.mgz to /subject/patient/mri/orig/001.mgz and rerunning recon-all. The orig.mgz file is created later on in the recon-all stream. -Louis On Thu, 17 Jan 2013, Louis Nicholas Vinke wrote: Please remember to cc the list. -- Forwarded message -- Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET) From: zach.p...@post.cz To: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Subject: Re: Re: [Freesurfer] nu_correct problem Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web page (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi, Documentation) I´ll send recon-all.log file later on I have it on another PC. Orig.mgz file - thats also problem. What I did: when running recon-all -subjid name -autorecon1 I get error: no /mri/orig/orig.mgz file. I looked into patients /mri directory and this path and file is not there. So that I created directory /orig in /mri and copied there converted patient.mgz file there and renamed it to orig.mgz. So that I have /subject/patient/mri/orig/orig.mgz. Maybe thats what is wrong? How do you get normally orig.mgz file? Thanks, Petr -- Původní zpráva -- Od: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Datum: 16. 1. 2013 Předmět: Re: [Freesurfer] nu_correct problem Hi Petr, Can you provide us with some more details? Which version of FreeSurfer are you using and on what platform? Could you attach a copy of the recon-all.log file for one of these cases so we can read the full error reported? Have you tried looking at the orig.mgz which is generated prior to the mri_nu_correct.mni step to see if it looks reasonable? -Louis On Wed, 16 Jan 2013, zach.p...@post.cz wrote: Dear members, when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu_correct. This happens for DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? Thanks much, Petr Zach 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] pial not computing
Hi Freesurfers, I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m ___ 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] pial not computing
Hi Mia we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote: Hi Freesurfers, I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m ___ 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] WM of lobes
You will need to create an annotation of the lobes (use mri_annotation2label --lobesStrict, or define your own). Then run mri_aparc2aseg with the --labelwm option. You can look in a recon-all.log for the other command options doug On 01/17/2013 07:54 AM, Gabriel Gonzalez Escamilla wrote: Dear freesurfers I'm trying to get the WM parcellation by lobes, I have read some previous FS archives regarding a similar topic, but they only want the volume value, and I'm interested in a WM lobes parcellation in mgz format (like aseg.mgz ), and I'm also interested in knowing if is possible to obtain this lobar parcellation for only cortical WM. Many thanks in advanced, Gabriel ___ 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] pial not computing
Hi Mia this is fixed in the newest version. You can grab a new mris_topo_fixer and you rerun and it should be all set. You probably should take a look at the ?h.orig.nofix to make sure it's reasonable (meaning no cerebellum or skull attached, and the hemispherees successfully separated) cheers Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote: Okay, so it didn't complete without error. I've attached the recon-all.log. Also, I was using another post op patient's MRI scans. thanks so much, m From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Thursday, January 17, 2013 11:22 AM To: Borzello, Mia Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] pial not computing Hi Mia we need to see the recon-all.log. Did it end with an error? Bruce On Thu, 17 Jan 2013, Borzello, Mia wrote: Hi Freesurfers, I just ran a recon, and it seems that only the lh.pial computed, but not the rh.pial. What would be the cause of this? Thanks, m ___ 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 ___ 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] long_mris_slopes / mris_calc problem
Hello Freesurfer experts, I am working on a study that wants to compare pre/post cortical thickness on an intervention group and a control group. I am using FS 5.1 on a Mac. I have processed all the recons through the longitudinal stream as described in the wiki/tutorial. However when I go to prepare the data using this command: long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years --qcache fsaverage It seems to run fine at first but after a minute or so it hits this command and crashes: mris_calc -o /Applications/freesurfer/subjects/SPIN073/surf/lh.long.thickness-spc.fwhm0.mgh ./tmp-SPIN073_lh_thickness_igG3e9/beta1.mgh div ./tmp-SPIN073_lh_thickness_igG3e9/beta0.mgh It prints: ERROR 1 : mris_calc compute sym. pct. change (spc) problem? And then returns to my command prompt. I searched online and found someone last year asked the same question here: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2011-September/020311.html However the response links to an updated version of mris_calc but when I click the link it says I do not have permission the access. Thanks for any help in advance. -Andrew ___ 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] edit or not to edit?
Hi FreeSurfer folks, we are about to process about 120 images with FS v5.1 and stand in front of a decision whether to do manual intervention or use the results from fully-automated FS run. We intend to use the volume, thickness, area, curvature measures of subcortical and cortical regions and were hoping to receive some advice on this dilemma: /to edit / or/not to edit/? Our data is decent quality, of healthy children (6-9 years old) and adults, acquired on 3T GE scanner, FSPGR sequence, with TI=400ms, TR=8.5ms, TE=3.4ms, flip angle=15deg, resolution 0.86 x 0.86 x 1.2mm, one scan per subject. I understand that visual inspection of the results is necessary in either case. If there were gross errors detected, would you advise to exclude the subject from analysis or rather do manual editing on these subjects that need it? Any and all thoughts or comments that could help us with the decision are most appreciated! Thank you! Miro Drahos http://brainlens.org ___ 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] problem with AutoReco3 mapping
I did an AutoRecon3 on a brain and when i viewed the results. it failed to classify some the tgray and white matter in the left hemisphere. the area misses is on the extreme left side of the brain, within 10 mm of the left side of the hemisphere. are there some arguments i change change to fix this. Jon Wieser jonwie...@netzero.com When the going gets tough, switch to power tools. - Red Green One Trick to Stay Asleep If you struggle to fall asleep, or stay asleep, try this#8230 http://thirdpartyoffers.netzero.net/TGL3241/50f85712990b57112b48st01duc ___ 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] nu_correct problem (fwd)
Hallo, now I use cc... Actually I gave you wrong info - I DID rename file patient.mgz to 001.mgz and not orig.mgz as I wrote before, sorry. I attach recon-all.log file with errors from my last run. It is about nu_ correct. Thanks for help, Petr -- Původní zpráva -- Od: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Datum: 17. 1. 2013 Předmět: Re: [Freesurfer] nu_correct problem (fwd) Hi Petr, Try renaming /subject/patient/mri/orig/orig.mgz to /subject/patient/mri/orig/001.mgz and rerunning recon-all. The orig.mgz file is created later on in the recon-all stream. -Louis On Thu, 17 Jan 2013, Louis Nicholas Vinke wrote: Please remember to cc the list. -- Forwarded message -- Date: Thu, 17 Jan 2013 11:07:43 +0100 (CET) From: zach.p...@post.cz To: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Subject: Re: Re: [Freesurfer] nu_correct problem Hallo, I use VB Ubuntu on standard PC machine downloaded from Freesurfer web page (freesurfer-Virtualbox-linux-x86-stable-pub-v5.1.0-full.vdi, Documentation) I´ll send recon-all.log file later on I have it on another PC. Orig.mgz file - thats also problem. What I did: when running recon-all -subjid name -autorecon1 I get error: no /mri/orig/orig.mgz file. I looked into patients /mri directory and this path and file is not there. So that I created directory /orig in /mri and copied there converted patient.mgz file there and renamed it to orig.mgz. So that I have /subject/patient/mri/orig/orig.mgz. Maybe thats what is wrong? How do you get normally orig.mgz file? Thanks, Petr -- Původní zpráva -- Od: Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu Datum: 16. 1. 2013 Předmět: Re: [Freesurfer] nu_correct problem Hi Petr, Can you provide us with some more details? Which version of FreeSurfer are you using and on what platform? Could you attach a copy of the recon-all.log file for one of these cases so we can read the full error reported? Have you tried looking at the orig.mgz which is generated prior to the mri_nu_correct.mni step to see if it looks reasonable? -Louis On Wed, 16 Jan 2013, zach.p...@post.cz wrote: Dear members, when I run recon_all -subjid name -autorecon1 process stops with ERROR at nu_correct. This happens for DICOM but also IMA file type. I tried several brains. Do you have any idea what is wrong? Thanks much, Petr Zach 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. Thu Jan 17 14:40:30 EST 2013 /home/virtualuser/freesurfer/subjects/s /home/virtualuser/freesurfer/bin/recon-all -subjid s -autorecon1 subjid s setenv SUBJECTS_DIR /home/virtualuser/freesurfer/subjects FREESURFER_HOME /home/virtualuser/freesurfer Actual FREESURFER_HOME /home/virtualuser/freesurfer build-stamp.txt: freesurfer-Linux-centos4-stable-pub-v5.1.0 Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux cputime unlimited filesize unlimited datasize unlimited stacksize8192 kbytes coredumpsize 0 kbytes memoryuseunlimited vmemoryuse unlimited descriptors 1024 memorylocked 64 kbytes maxproc unlimited total used free sharedbuffers cached Mem:458880 306100 152780 0 31844 134440 -/+ buffers/cache: 139816 319064 Swap: 530104 0 530104 program versions used $Id: recon-all,v 1.395 2011/05/18 23:01:39 krish Exp $ $Id: mri_motion_correct.fsl,v 1.14 2011/03/02 20:16:39 nicks Exp $ mri_convert -all-info ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:31-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400 FLIRT version 5.5 $Id: talairach_avi,v 1.9 2011/03/02 18:38:06 nicks Exp $ mri_convert --version stable5 ProgramName: tkregister2_cmdl ProgramArguments: --all-info ProgramVersion: $Name: stable5 $ TimeStamp: 2013/01/17-19:40:32-GMT BuildTimeStamp: May 16 2011 12:54:49 CVS: $Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $ User: virtualuser Machine: FreeSurfer Platform: Linux PlatformVersion: 2.6.28-11-generic CompilerName: GCC CompilerVersion: 30400 Program nu_correct, built from: Package MNI N3, version 1.10, compiled by nicks@fishie (i686-pc-linux-gnu) on
[Freesurfer] Merging .annot files
Hello all, I posted this question on the cmtk users google group, but no takers, and perhaps this is the more appropriate venue anyways. I've been successfully using cmtk within iPython. After running connectomemapper parcellate() to get the Lausanne parcellation scheme, I get six .annot files: ?h.myaparcP1_16.annot, ?h.myaparcP17_28.annot, and ?h.myaparcP29_66.annot, for each of lh and rh. Each of these .annot files label the entire cortical surface, but each of the 36 major anatomical regions (e.g., posteriorcingulate) for each hemisphere are further subdivided in only one of the three .annot files; the other two files use the original definition of the major region. In other words, in order to use these .annot files to work with the Lausanne sub-parcellations for the entire cortical surface, one has to run the same procedure using each of the 3 .annot files, and then figure out which .annot file provided the desired information. I was wondering whether it is possible to merge the three annot files to create a single .annot file for each hemisphere in which ALL of the 36 major anatomical regions have been subdivided, rather than three files containing parcellations of different subsets of these regions? Though I have been using scripts to sift through multiple sets of results to find what I'm looking for, some manual chores would be easier if I only had to work with a single file. The fact that the same vertices are labeled in all files (but are given the macro-region label in 2 files, and the sub-parcelation label in 1 file) makes me think that it's not a simple matter of concatenating the annotation files. Thanks, Chris ___ 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] Freesurfer vertex wise area reference
Dear Mahinda, For the mris_preproc, I think Doug posted already explaining how it works - it uses a jacobian correction in a way that makes it mass-conservative. You may want to search the archives. For the ROIs, the standard method is to add up the areas of their constituent vertices, so it should be straightforward to describe I believe. And the statistics are based on the GLM, which is already well entrenched in the literature, with no need for details other than describing carefully the design you used and how you corrected for multiple testing. About a general discussion on area, the methods, etc, then yes, that would be the paper that you know already. All the best, Anderson 2013/1/17 MAHINDA YOGARAJAH y.mahi...@gmail.com Hi, Sorry to be a little more specific - I am aware of freesurfer area references such as the WInkler reference but basically wanted a few lines, and the most appropriate references, that summarises the technical approach used for group area comparisons in qdec (using updated mris_preproc), and simple ROI group area comparisons. Thanks, Mahinda ___ 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.
