Freesurfer

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30090 discussions

Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview
by Ursula Tooley 19 Jul '17

19 Jul '17

Hi Ruopeng, That works perfectly, thanks so much. Best, Ursula --- Ursula Tooley Ph.D. Student Neuroscience Graduate Group University of Pennsylvania utooley(a)gmail.com 202.413.5627 > > From: Ruopeng Wang <rpwang(a)nmr.mgh.harvard.edu <mailto:rpwang@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Custom Annotation: 1st Annot Visible in TKSurfer but not Freeview > Date: July 17, 2017 at 11:43:18 AM EDT > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > > > Hi Ursula, > > Since FS 6.0, freeview stopped displaying index 0 in the annotation look up table which is usually reserved as "unknown 0 0 0 0", so that it doesn't show a black region on the surface. Would it be possible for you change your indices starting from 1? I will also update freeview so that it can check the color of index 0 and handle it more smartly. > > Best, > Ruopeng > > On 07/14/2017 06:10 PM, Ursula Tooley wrote: >> Hi FreeSurfer Experts, >> >> I’ve created a custom annotation file in MATLAB, using read_annotation.m and write_annotation.m, relabeling the Glasser parcellation regions. It seems to display as expected in tksurfer and tkmedit, but in freeview the first annotation is completely transparent (see images below), although if I hover my mouse over the area, it’s labeled with the correct struct_name. I’ve changed the alpha value in the annotation file and see no difference in freeview, and also given some previous listserv posts tried changing the RGB values for that first annotation in colortable.table. >> >> View in tksurfer: >> tksurfer fsaverage lh inflated -annotation my_annotation.annot >> >> View in freeview: >> freeview $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=my_annotation.annot >> >> Any help would be greatly appreciated. I’m running FS 6.0, Freeview V2, this occurs both locally on my OSX El Capitan and on an HPC running Linux Centos. >> >> Thanks in advance, >> Ursula >> >> >> >> >> >> >> --- >> Ursula Tooley >> Ph.D. Student >> Neuroscience Graduate Group >> University of Pennsylvania >> utooley(a)gmail.com <mailto:utooley@gmail.com> >> 202.413.5627 >> >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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 <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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Recon-all start point for pial, aseg, CP edits
by Eric Mitchell 19 Jul '17

19 Jul '17

Hi developers, I am working with scans from a group of patients that sometimes require pial edits, aseg editing (e.g. ventricle being labelled as amygdala), and control points to fix intensity normalizations. I am unsure as to which stage I should start the recon-all re-processing at so that it will take into account all the edits. Thanks, Eric Mitchell This email is directed in confidence solely to the person named above and may contain confidential, privileged or personal health information. Please be aware that this email may also be released to members of the public under Ontario's Freedom of Information and Protection of Privacy Act if required. Review, distribution, or disclosure of this email by anyone other than the person(s) for whom it was originally intended is strictly prohibited. If you are not an intended recipient, please notify the sender immediately via a return email and destroy all copies of the original message. Thank you for your cooperation.

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Re: [Freesurfer] Switch FreeSurfer Desikan-Killiany atlas to Civet
by Antonin Skoch 19 Jul '17

19 Jul '17

Dear Trisanna, thank you for the reference. However, I did not find any specific information in this paper what specific methods are used in CIVET and what is the difference in implementation between CIVET and FreeSurfer. Antonin I believe the cortical thickness measures are taken slightly differently. This paper might offer some insights.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4408913/ Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology On Fri, Jul 14, 2017 at 8:29 AM, Antonin Skoch <a...(a)ikem.cz> wrote: > Dear Zhiquiang, > > as a regular user of FreeSurfer I am wondering, what is the advantage of > using Civet instead of FreeSurfer? > > Are there some functionalities in Civet which are not available in > FreeSurfer? > Or does Civet offer better performance/accuracy/precision in estimation of > surface models for some situations/datasets? > > Antonin Skoch > > > Hello FreeSurfer Developers, > > I am attempting to switch the Desikan-Killiany atlas of FreeSurfer to Civet. > But I have no idea to solve the problem. Would you like to give me some > suggestions or some detailed steps to help me accomplish the tasks ? > > > Best wishes, > Zhiqiang Sha >

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Re: [Freesurfer] dmri_motion -T threshold
by Yendiki, Anastasia 19 Jul '17

19 Jul '17

If neither of your groups has bad slices (which you should confirm by looking at the images), then they are matched in that respect. You can then check for differences in the rotational and translational motion to see if any further matching is needed. From: <freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of "Buckless, Colleen" <Buckless(a)kennedykrieger.org<mailto:Buckless@kennedykrieger.org>> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, July 19, 2017 at 9:14 AM To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] dmri_motion -T threshold Hi Anastasia, We are trying to match our groups on motion and can’t match them if our scans have the floor values. We are not sure how to determine what the threshold value should be in order to make the dropout score no longer floor out. Any suggestions on how to better match on motion? Thanks, Colleen From: freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Tuesday, July 18, 2017 6:46 PM To: Freesurfer support list Subject: Re: [Freesurfer] dmri_motion -T threshold Hi Colleen - Do the DWIs of your subjects have any slices that are in the brain but look very dark, almost like the background? That's what those measures capture, and not all subjects have that. If your subjects don't have that, then there's nothing to be concerned about! Best, a.y ________________________________ From:freesurfer-bounces@nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu> [freesurfer-bounces(a)nmr.mgh.harvard.edu<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>] on behalf of Buckless, Colleen [Buckless(a)kennedykrieger.org<mailto:Buckless@kennedykrieger.org>] Sent: Friday, July 14, 2017 3:35 PM To: 'freesurfer(a)nmr.mgh.harvard.edu<mailto:'freesurfer(a)nmr.mgh.harvard.edu>' Subject: [Freesurfer] dmri_motion -T threshold Hi All, I've been using dmri_motion to quantify motion in our DTI data. We are uncertain how to determine what the –T threshold should be. We have read through the wiki and the related papers and are confused what this number represents, how it effects the output, and the rational for selecting a specific threshold value. We have tried the default (100) and almost all of our scans have the floor values (0 and 1) for percent bad slices and average dropout score, and we are concerned that this value is most likely inappropriate for our data. We have tried other values but are unsure what a suitable threshold value should be for our data. We are concerned that this number effects the output, and want to make sure we are using an appropriate value. What is the best way to select the –T threshold and the rational for selecting one value versus another? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless(a)kennedykrieger.org<mailto:Buckless@kennedykrieger.org> ________________________________ Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Masking option for tractstats2table
by Derek A Pisner 19 Jul '17

19 Jul '17

Hi Anastasia or Krish, Is there a version of tractstats2table floating around that allows me to apply a binarized mask to extract stats for sub-sections of tracts? If not, I can write my own—just wanting to see if such a function already exists so that I don’t reinvent the wheel… Derek Pisner Doctoral Student CLA 4.600 Mood Disorders Laboratory (MDL) Department of Psychology | The University of Texas at Austin

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dmri_motion -T threshold
by Buckless, Colleen 19 Jul '17

19 Jul '17

Hi All, I've been using dmri_motion to quantify motion in our DTI data. We are uncertain how to determine what the -T threshold should be. We have read through the wiki and the related papers and are confused what this number represents, how it effects the output, and the rational for selecting a specific threshold value. We have tried the default (100) and almost all of our scans have the floor values (0 and 1) for percent bad slices and average dropout score, and we are concerned that this value is most likely inappropriate for our data. We have tried other values but are unsure what a suitable threshold value should be for our data. We are concerned that this number effects the output, and want to make sure we are using an appropriate value. What is the best way to select the -T threshold and the rational for selecting one value versus another? Thanks, Colleen Buckless Research Assistant Center for Neurodevelopmental and Imaging Research Kennedy Krieger Institute 443-923-2747 Buckless(a)kennedykrieger.org ---------------------------------------------------------------------- Disclaimer: The materials in this e-mail are private and may contain Protected Information. Please note that e-mail communication is not encrypted by default. You have the right to request further emails be encrypted by notifying the sender. Your continued use of e-mail constitutes your acknowledgment of these confidentiality and security limitations. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying, distribution, or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this e-mail in error, please immediately notify the sender via telephone or return e-mail.

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Re: [Freesurfer] what program generates "path.map.txt" for dmri_pathstats to run?
by Yuwen Hung 18 Jul '17

18 Jul '17

Dear DTI experts: I am wondering if anybody could provide any information to help me out with this constant error that I am desperate to resolve? I just need to know what program generates this "path.map.txt" for the tracula script dmri_pathstats to run through? dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug cwd /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610 cmdline dmri_pathstats --intrc START_610/dpath/lh.cst_AS_avg33_mni_bbr --dtbase START_610/dmri/dtifit --path lh.cst --subj START_610 --out START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt --outvox START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt --debug sysname Linux hostname node031 machine x86_64 user yuwenh Input tracula directory: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr Input DTI fit base: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dmri/dtifit Pathway name: lh.cst Subject name: START_610 Output file for overall measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.overall.txt Output file for voxel-by-voxel measures: /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/pathstats.byvoxel.txt Lower threshold for probability: 0.200000 Computing statistics on /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr... ERROR: Could not open /gablab/p/START/NEW_DTI_ANALYSIS_2017/START_610/START_610/dpath/lh.cst_AS_avg33_mni_bbr/path.map.txt for reading Your help is being greatly appreciated, Yuwen -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of freesurfer-request(a)nmr.mgh.harvard.edu Sent: Friday, July 14, 2017 4:14 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: Freesurfer Digest, Vol 161, Issue 25 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: PETsurfer AC/TOF (Douglas N Greve) 2. Re: 3G1V.fsgd (Douglas N Greve) 3. Re: GLM Analysis Number of vertices and Area (Douglas N Greve) 4. Regression diagnostic in context of surface-based analysis (Antonin Skoch) 5. bbregister + mri_vol2vol different results (Paul Glad Mihai) 6. R: Re: 3G1V.fsgd (stdp82(a)virgilio.it) 7. R: R: Re: 3G1V.fsgd (stdp82(a)virgilio.it) 8. Re: R: Re: 3G1V.fsgd (Douglas N Greve) 9. Mid point on Freeview (Trisanna Sprung-Much) 10. vertex-wise contra-lateral mapping on an ico surface (Burke Rosen) 11. Re: Mid point on Freeview (Bruce Fischl) 12. Re: ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness (M Janani) 13. R: Re: R: Re: 3G1V.fsgd (stdp82(a)virgilio.it) 14. problems with recon-all in 6.0 (Lars M. Rimol) ---------------------------------------------------------------------- Message: 1 Date: Thu, 13 Jul 2017 16:28:24 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] PETsurfer AC/TOF To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <d5234734-a0cc-e310-cd02-d73229c9437c(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed Sorry, I don't know what the difference is. I always use the mean update volume as the template for registration. On 07/13/2017 01:57 PM, Fu, Jason (NIH/NINDS) [F] wrote: > ac/tof is attenuation corrected/time of flight. Ac/hd is attenuation corrected/head. > > -----Original Message----- > From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Sent: Thursday, July 13, 2017 12:52 PM > To: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] PETsurfer AC/TOF > > sorry, what is an ac/tof file? > > > On 07/13/2017 12:12 PM, Fu, Jason (NIH/NINDS) [F] wrote: >> Hi, >> >> I am currently using PETsurfer PVC to determine glucose metabolism >> differences in certain structures between the brain hemispheres. I am >> currently using ac/tof files to coregister to the anatomy. One of the >> patients did not have the ac/tof files, would ac/hd files work instead? >> >> Thanks, >> Jason Fu >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 2 Date: Thu, 13 Jul 2017 16:30:54 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] 3G1V.fsgd To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1139ca82-1846-fbb5-9650-f10a5ad867c4(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed On 07/13/2017 10:37 AM, stdp82(a)virgilio.it wrote: > Dear FS group, > > I don't understand how I should build the contrast for 3 groups 1 > covariate. > No specific example is provided within fsgd example and also other > colleagues report the same problem in the mail list. > Please could you provide us details on this topic? > Especially, how should be the g3v1.intercept and g31v.slope? > > 1 -1 0 0 0 0 > 1 0 -1 0 0 0 > for g3v1.intercept.mtx This is the main effect of group on the intercept regressing out the effect of covariate. > > and > 0 0 0 1 -1 0 > 0 0 0 1 0 -1 > for g3v1.slope.mtx This is the main effect of group on the slope regressing out the effect of group intercept. > > > are corrected? > > Waiting for you very wellcome suggestions > > Thanks and kind regards > > Stefano > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 3 Date: Thu, 13 Jul 2017 16:38:21 -0400 From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] GLM Analysis Number of vertices and Area To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <7ef1f42e-31d6-fe1e-7e89-9e04338a8a9d(a)nmr.mgh.harvard.edu> Content-Type: text/plain; charset=utf-8; format=flowed I'm not sure what you mean. Do you want stats for every cluster regardless of significance? If so, you can run the monte carlo correction with a clusterwise p-value (--cwp in mri_glmfit-sim) of 1.0 On 07/13/2017 11:52 AM, Aman Montazeri wrote: > Hello Friends, > > Sorry for the simple question. > > I am doing GLM analysis using QDEC between two groups (one discrete > variable), then I run the Monte-Carlo clustering and got the stats of > my cluster. > > My supervisor asked me to get the Stats of blobs/clusters (area and > number of vertices in each area) before applying the Monte-Carlo (only > after GLM analysis/comparison) > I would really appreciate if you could help me with getting those > stats, as I can't figure out how to do it. > > > Thank you, > Aman > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ------------------------------ Message: 4 Date: Thu, 13 Jul 2017 22:48:03 +0200 From: Antonin Skoch <ansk(a)ikem.cz> Subject: [Freesurfer] Regression diagnostic in context of surface-based analysis To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <1034294575-17116(a)posta.medicon.cz> Content-Type: text/plain; charset="utf-8" Dear experts, I am looking for a way how to effectively run a regression model diagnostic in context of surface-based analysis. My example case is the regression model where response variable is cortical thickness and explanatory variable is continuous (disease duration). The statistical linear modelling uses several principial approaches to find model which best describes the studied relation in the data, namely: 1. model simplification by elimination of insignificant effects 2. transformation of dependent variable to improve normality of residuals 3. transformation of explanatory variable to improve model fit or use of linear combination of various terms in explanatory variable (for example apart from linear term to include also quadratic and higher-order polynomial terms) My question is, how to effectively exploit methods 2 and 3 in context of vertex-wise surface-based analysis? Could you please comment on what tools inside FreeSurfer framework can be used for this purpose? What is your common aproach to find regression model which best approximates the relation present in the data? Thank you in advance for pointing me to right direction. Regards, Antonin Skoch

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WM edits not being applied to surfaces
by Dan Grupe 18 Jul '17

18 Jul '17

Hi all, We are making manual white matter edits using the "voxel edit" tool in freeview with “recon editing” selected. These edits are being saved to wm.mgz but not applied to the white matter surfaces (using the command: recon-all -autorecon2-wm -autorecon3 -subjid). We are using FreeSurfer v5.3 on OS X version 10.11.6. I have seen this question posed by others on the message board in the last few months, but haven’t figured out if there is a known solution. Thanks for any suggestions or support! -Dan ------ Dan Grupe, Ph.D. Assistant Scientist Center for Healthy Minds University of Wisconsin-Madison ------ grupe(a)wisc.edu<mailto:grupe@wisc.edu> 608-263-7572 http://brainimaging.waisman.wisc.edu/~dgrupe

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mris_label2annotation error
by francesca bottino 18 Jul '17

18 Jul '17

Hello FreeSurfer Developers, I'm attempting to convert only one file.label in one file.annot. I'm using the command MRIS_LABEL2ANNOTATION. mris_label2annot --s fsaverage --h lh --l '/home/mlucignani/Desktop/TUTTO/merge/MERGE_AREA_1/originali_lh/lh_FILE_1.label' ERROR: need to specify color table file I don't know wich color table file insert

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Re: [Freesurfer] ERROR: dimension mismatch between input volume and seg - VolumeROICorticalThickness
by M Janani 18 Jul '17

18 Jul '17

Hi Douglas Greve, Yes, I'm getting the same result as mentioned below. Regards, Janani ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Did you get exactly the same error? On 07/14/2017 02:05 AM, M Janani wrote: > > Hi Douglas Greve > <https://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from…>, > > Thanks for your support. > > I tried with the --reshape-factor 6. But it didn't work for me. > > The segmentation was created using the below mentioned data > > 1.SPM standard ROI > > 2..dat file generated using the T1.nii(available in SPM8 template) and > fsaverage. > > Please help us to proceed further. > > Regards, > > Janani > > ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > How did you create the segmentation? You can change the shape of the > seg with mri_surf2surf --reshape 6 --s fsaverage --hemi lh --sval > seg.mgh --tval seg.reshape.mgh > > On 7/7/17 10:15 AM, M Janani wrote: > Hi Team, > > I'm attempting to extract cortical thickness values for a > region-of-interest (ROI) defined in volume spacesubject for PiB MRI. > > I got the below mentioned error while computing the stats value > cwd > > cmdline mri_segstats --seg > freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh --in > lh.thickness.fsaverage.mgh --sum segstats-CBLROI.txt > > sysname Linux > hostname teslak80 > machine x86_64 > user lakshman > UseRobust 0 > Loading /freesurfer/subjects/fsaverage/surf/lh.fsaverage.CBLROI.mgh > Loading lh.thickness.fsaverage.mgh > ERROR: dimension mismatch between input volume and seg > input 27307 1 6 > seg 23406 1 7 > > I tried with the solution provided in the below mail, but it didn't > work for me > > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-January/027405.…<https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> > > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> > > <https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027405.h…> > > Any help would be really helpful. > Regards, > Janani > ::DISCLAIMER:: > ---------------------------------------------------------------------------------------------------------------------------------------------------- > > The contents of this e-mail and any attachment(s) are confidential and > intended for the named recipient(s) only. E-mail transmission is not > guaranteed to be secure or error-free as information could be > intercepted, corrupted, lost, destroyed, arrive late or incomplete, or > may contain viruses in transmission. The e mail and its contents (with > or without referred errors) shall therefore not attach any liability > on the originator or HCL or its affiliates. Views or opinions, if any, > presented in this email are solely those of the author and may not > necessarily reflect the views or opinions of HCL or its affiliates. > Any form of reproduction, dissemination, copying, disclosure, > modification, distribution and / or publication of this message > without the prior written consent of authorized representative of HCL > is strictly prohibited. If you have received this email in error > please delete it and notify the sender immediately. Before opening any > email and/or attachments, please check them for viruses and other > defects. > > ---------------------------------------------------------------------------------------------------------------------------------------------------- > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ > 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. > > > > _______________________________________________ > 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 gr...(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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