Freesurfer October 2012

freesurfer@nmr.mgh.harvard.edu

119 participants
191 discussions

Re: [Freesurfer] Comparing thickness at vertex level
by Douglas N Greve 24 Oct '12

24 Oct '12

they will have the same number of vertices. They will all be in one file, and each vertex is a vertex in fsaverage space, which each subject vertex being mapped to the closest vertex in surface-based atlas. doug On 10/24/2012 04:34 PM, Gabriel Gonzalez Escamilla wrote: > Thanks Doug, > > Does the surface-based thickness approach make possible to compare > exactly the same vertex across all my subjects? or they will be still > have some differences in the number of vertices among them? > > Gabriel > > > El 24/10/12, *Douglas N Greve * <greve(a)nmr.mgh.harvard.edu> escribió: >> Hi Gabriel, this sounds like a standard surface-based thickness study. >> Or am I missing something? In case it is, you can look at the group >> analysis tutorial. Basically, you run mris_preproc (which puts all of >> your subjects into the fsaverage space and saves a stack of thickness >> maps in a single file), then you smooth it, then you run mri_glmfit. >> >> doug >> >> On 10/24/2012 11:47 AM, Gabriel Gonzalez Escamilla wrote: >> > >> > Dear FreeSurfer experts, >> > >> > I'm wondering if is it possible to make vertex to vertex comparisons >> > for thickness on a group of subjects. In other words, I have a bunch >> > of subjects pre-processed with FS but I would like to make comparisons >> > finding the thickness values at same vertex in all of them. Is this >> > possible with Freesurfer? >> > >> > Given that at the beggining all they have different head/brain sizes, >> > I was thinking that a regristration of the surfaces to the same space >> > (FSaverage) would re-sample my data to match in number of vertex. for >> > this, I think that maybe "mri_surf2surf" is capable of such a thing, >> > and then I would have to search for each vertex, or optionally >> > "mris_preproc" using the "-target FSaverage" flag ||*||*would perform >> > something similar. >> > >> > Please tell me what you think about this? >> > >> > >> > Many thanks in advanced, >> > Gabriel. >> > >> > >> > _______________________________________________ >> > Freesurfer mailing list >> > Freesurfer(a)nmr.mgh.harvard.edu >> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the sender >> and properly >> dispose of the e-mail. >> > > -- > -------------------------- > PhD. student Gabriel González-Escamilla > Laboratory of Functional Neuroscience > Department of Physiology, Anatomy, and Cell Biology > University Pablo de Olavide > Ctra. de Utrera, Km.1 > 41013 - Seville > - Spain - > > Email: ggonesc(a)upo.es > http://www.upo.es/neuroaging/es/ -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] mris_topo_fixer -mgz -warnings -seed 1234
by Anne Uhlmann 24 Oct '12

24 Oct '12

Hi Bruce, I am running freesurfer-Linux-centos4_x86_64-stable-pub-v4.5.0 on a cluster (which I access via putty). It's the only scan that has some kind of a scanner artifact and that shows this particular problem, therefore I thought there might be a link. Thanks, Anne >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 24/10/2012 13:42 >>> Hi Anne can you cc the list so others can answer? What version are you running? This is something we fixed a while ago cheers Bruce On Wed, 24 Oct 2012, Anne Uhlmann wrote: > Hi Bruce, > > Sorry about that. Please find the recon-all.log file attached. The error > message given there is: ERROR: _FindFacePath: could not find path! > > No rh output is getting produced. > When viewing the brainmask.mgz -surfs, an error message says: rh.white: > could not open file. > > When trying to view rh.orig.nofix, the error message says: rh.pial: no such > file or directory. But the wm outline looks just like the lh one, very > angular but otherwise no defects. Sometimes voxels are included that should > not be white matter and in the occipital area some of the white matter is > excluded. > > I can't say much about the rh.inflated.nofix. I can only view it in tkmedit > and it seems to have some fine disruptions in the occipital area. > > Thanks for your help. > Regards, Anne > > > > > >>> Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 22/10/2012 15:50 >>> > Hi Anne > > can you post the whole recon-all.log file? I don't think you included the > actual error message. Also, you can look at the rh.inflated.nofix and > rh.orig.nofix to see if there are any really big defects in the rh before > fixing. Is no rh output produced? > > Bruce > > On Mon, 22 Oct 2012, Anne Uhlmann wrote: > > > Hi there, > > > > I am having trouble with one of my scans where the right hemisphere is not > > getting included in the analysis from the "Fix Topology rh" point on. This > > is the error message I get: > > > > Linux cnode-2-52 2.6.18-308.el5 #1 SMP Tue Feb 21 20:06:06 EST 2012 x86_64 > > x86_64 x86_64 GNU/Linux > > $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ > > /SCRATCH4/cubic/auhlmann/freesurfer/bin/recon-all > >PWD/lustre/SCRATCH4/cubic/auhlmann/freesurfer/subjects/meth_output_test3/MA > S11 > > 2.12.1107.5.2/scripts > > CMD mris_topo_fixer -mgz -warnings -seed 1234 MAS112.12.1107.5.2 rh > > > > The orig.mgz looks OKish (it's not great) except for some kind of a > scanner > > artifact in 2 slices of the scan. I tried to fix it with control points > and > > making edits to the white matter, but unfortunately it didn't solve the > > problem. I am grateful for any suggestions. > > > > Thank you and best regards, > > Anne > > > > ### > > > > UNIVERSITY OF CAPE TOWN > > > > This e-mail is subject to the UCT ICT policies and e-mail disclaimer > > published on our website at > > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from > +27 > > 21 650 9111. This e-mail is intended only for the person(s) to whom it is > > addressed. If the e-mail has reached you in error, please notify the > author. > > If you are not the intended recipient of the e-mail you may not use, > > disclose, copy, redirect or print the content. If this e-mail is not > related > > to the business of UCT it is sent by the sender in the sender's individual > > capacity. > > > > ### > > > > > > > > > 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. > > ### > > UNIVERSITY OF CAPE TOWN > > This e-mail is subject to the UCT ICT policies and e-mail disclaimer > published on our website at > http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 > 21 650 9111. This e-mail is intended only for the person(s) to whom it is > addressed. If the e-mail has reached you in error, please notify the author. > If you are not the intended recipient of the e-mail you may not use, > disclose, copy, redirect or print the content. If this e-mail is not related > to the business of UCT it is sent by the sender in the sender's individual > capacity. > > ### > > > ### UNIVERSITY OF CAPE TOWN This e-mail is subject to the UCT ICT policies and e-mail disclaimer published on our website at http://www.uct.ac.za/about/policies/emaildisclaimer/ or obtainable from +27 21 650 9111. This e-mail is intended only for the person(s) to whom it is addressed. If the e-mail has reached you in error, please notify the author. If you are not the intended recipient of the e-mail you may not use, disclose, copy, redirect or print the content. If this e-mail is not related to the business of UCT it is sent by the sender in the sender's individual capacity. ###

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task-related functional connectivity analyses freesurfer 5.1.0
by SHAHIN NASR 24 Oct '12

24 Oct '12

Hi, I was wondering if we can compare "functional connectivity" between blocks within a run as we do for BOLD signal using freesurfer. Current documentation of freesurfer is for resting state and does not consider conditions that experiment is Blocked Design. Similar question has been asked previous but nobody answered (see the link below) https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2012-June/024394.html Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

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Re: [Freesurfer] recon-all \'expression syntax\' error
by Skyler Gabriel Shollenbarger 24 Oct '12

24 Oct '12

Hi Bruce, I'm having the same error: export SUBJECTS_DIR=$PWD recon-all -subjid freesurfer -autorecon1 if: Expression Syntax. Running on: OS X 10.6.8 using both terminal and X11 (freesurfer-Darwin-leopard-i686-stable-pub-v5.0.0) Thanks in advance, Skyler -- Skyler G. Shollenbarger Graduate Student - UWM Brain Lab Clinical Psychology & Neurospychology University of Wisconsin-Milwaukee

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Comparing thickness at vertex level
by Gabriel Gonzalez Escamilla 24 Oct '12

24 Oct '12

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Total cerebral volume.
by Zheng Hui 24 Oct '12

24 Oct '12

Hi freesurfer, We are trying to calculate the total cerebral volume which excludes cerebellum, brainstem, ventricle and CSF from the aseg.txt. Do we use CortexVol + CorticalWhiteMatterVol + SubCortGrayVol Or CortexVol + CorticalWhiteMatterVol + Sum(all structures (after ICV in the list) except ventricle, CSF, cerebellum and brainstem) Also, I saw Doug's post about the bug fixing for SupraTentorialVol. To re-run the segstats for longitudinal subjects, any extra step other than "recon-all –long tpN baseID –segstats" and does it affect any other structure or just SupraTentorialVol? Thank you, Zheng Hui

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Re: [Freesurfer] AAL labels
by Garikoitz Lerma-Usabiaga 24 Oct '12

24 Oct '12

Hi! Well, as far as I know: - both are MNI standards ---- Colin27 is the MNI Colin27 single subject standard ---- fsaverage is MNI305 My problem with fsaverage was that I couldn't use the transformations made with the registration matrix after spmregister or bbregister, but I understand that it depends on the application. This is the reason I used the alternative way through Colin27 (since both are the same brain, one in 2mm and the other in 1mm, the registration matrix was almost 1). Saying that, I understand that if you want the AAL .labels in fsaverage, you always could use mri_label2label in order to transform every label to fsaverage. I don't know what is the best method, maybe some expert in the list will be able to confirm this step, but it is definitely what I would do. If you are thinking using qdec or some other tool with fsaverage, I understand that you could always create your own average and transform the data there or create the data with mri_surf2surf for Colin27 (this is going to be our approach). hope this helps! Gari On Tue, Oct 23, 2012 at 7:15 PM, MCLAREN, Donald <mclaren.donald(a)gmail.com>wrote: > How does the Colin 27 space differ from MNI space in terms of > freesurfer? Ideally, I'd want them to be useable with the standard FS > Average surface that is in MNI space. > > Best Regards, Donald McLaren > ================= > D.G. McLaren, Ph.D. > Research Fellow, Department of Neurology, Massachusetts General Hospital > and > Harvard Medical School > Postdoctoral Research Fellow, GRECC, Bedford VA > Website: http://www.martinos.org/~mclaren > Office: (773) 406-2464 > ===================== > This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED > HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > intended only for the use of the individual or entity named above. If the > reader of the e-mail is not the intended recipient or the employee or agent > responsible for delivering it to the intended recipient, you are hereby > notified that you are in possession of confidential and privileged > information. Any unauthorized use, disclosure, copying or the taking of any > action in reliance on the contents of this information is strictly > prohibited and may be unlawful. If you have received this e-mail > unintentionally, please immediately notify the sender via telephone at > (773) > 406-2464 or email. > > > On Tue, Oct 23, 2012 at 7:37 AM, Garikoitz Lerma-Usabiaga > <garikoitz(a)gmail.com> wrote: > > Hi Donald and everybody, > > I created AAL .mgh and .label-s in FS Colin27 space, if anybody is > > interested please drop me a line. > > > > best regards! > > Gari > > > > On Thu, Jul 12, 2012 at 11:12 PM, MCLAREN, Donald < > mclaren.donald(a)gmail.com> > > wrote: > >> > >> Has anyone created an AAL label file for Freesurfer? I've done some > >> ROI analysis using AAL regions and want to display regional values on > >> the freesurfer surface. > >> > >> Best Regards, Donald McLaren > >> ================= > >> D.G. McLaren, Ph.D. > >> Research Fellow, Department of Neurology, Massachusetts General Hospital > >> and > >> Harvard Medical School > >> Postdoctoral Research Fellow, GRECC, Bedford VA > >> Website: http://www.martinos.org/~mclaren > >> Office: (773) 406-2464 > >> ===================== > >> This e-mail contains CONFIDENTIAL INFORMATION which may contain > PROTECTED > >> HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is > >> intended only for the use of the individual or entity named above. If > the > >> reader of the e-mail is not the intended recipient or the employee or > >> agent > >> responsible for delivering it to the intended recipient, you are hereby > >> notified that you are in possession of confidential and privileged > >> information. Any unauthorized use, disclosure, copying or the taking of > >> any > >> action in reliance on the contents of this information is strictly > >> prohibited and may be unlawful. If you have received this e-mail > >> unintentionally, please immediately notify the sender via telephone at > >> (773) > >> 406-2464 or email. > >> _______________________________________________ > >> Freesurfer mailing list > >> Freesurfer(a)nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person to whom > it > >> is > >> addressed. If you believe this e-mail was sent to you in error and the > >> e-mail > >> contains patient information, please contact the Partners Compliance > >> HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was sent to you > in > >> error > >> but does not contain patient information, please contact the sender and > >> properly > >> dispose of the e-mail. > >> > > >

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Training-Control Group Comparison Analysis
by Ryan 24 Oct '12

24 Oct '12

Hello everyone, I'm conducting an analysis involving a training group and a control group, where each group has a pre and a post scan. I setup the matrix file, the contrast file, and ran mri_glmfit along with mri_glmfit-sim for the cluster correction. The analysis finished revealing a significant cluster, although I want to confirm that my interpretation of the results is correct. I see a significant cluster which I believe means the training group showed greater thickening compared to the controls, is this correct? Also, how can I tell if clusters represent thickening or thinning in the training group compared to the control group? When I setup the matrix file, I entered 1's and -1's for the control subjects in the first column, and training subjects in the second column. When I setup the contrast file, I entered a -1 and then a 1, with 0's for the rest of the variables. Thanks for the help. -W. Ryan McGarry

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direct repositioning
by pietro de rossi 24 Oct '12

24 Oct '12

Hi FreeSurfer people, I'm considering editing through direct repositioning in freeview (under tools->reposition surface) for some scans. After that, do I need to rerun everything through the whole recon-all pipeline? What would be the command line for that? Thank you very much, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Re: [Freesurfer] Changes to Sub-cortical Structures after adding WM control points
by Mark Fletcher 23 Oct '12

23 Oct '12

Do you know when the next version is slated to launch? That being said, if I wanted to salvage my work so far, is it best to just use the original "subcortical" output as is (if I was not trying to change it in the first place?). -Mark Fletcher On Wed, Oct 17, 2012 at 12:01 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu>wrote: > Hi Mark > > it's hard to say if it's a "bug", but it is definitely a change in > behavior that will go away with 5.2 (that is, we will no longer > regenerate the aseg when you add control points). > > cheers > Bruce > On Wed, 17 Oct 2012, Mark > Fletcher wrote: > > > Dear FreeSurfers, > > > > After adding WMCP to a number of my subjects (which corrected the > problem), > > I retrieved to cortical and subcortical volumes from my subjects using > the > > "aparcstats2table". I had used "aparcstats2table" before and after adding > > the control points. Accurately, the regions I wanted to change, did > change > > in volume. However, the subcortical volumes post WMCP changed a lot as > > well? Some regions changed more than 20% after adding WMCP to other > > regions? Is this normal? Should I go with the original "subcortical" > > segmentation volumes, or the new ones? Is this part of the known bug in > > version 5.1.0 mentioned in the release notes about "running recon-all" a > > second time? Please advise? > > > > Sincerely , > > Mark Fletcher > > > > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >

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Freesurfer October 2012