[Freesurfer] freeview errors

Hello, I sent in a message yesterday but to no avail. I thought I would add a little more info about the error message I'm receiving. I am trying to view surfaces in 3D using Freeview on my own subject data via this script from the Freesurfer website (replacing the subject name); freeview -f

[Freesurfer] make average explanation

Hello, I am currently trying to visualize group differences in cortical thickness across subject groups. In addition to using the qdec GUI, I am playing with the make_average_surface command as well as the make_average_subject command to then visualize in freeview or tksurfer - though I'm quite

[Freesurfer] qdec group analysis error

Hello there, I am trying to run an analysis in qdec with 25 subjects, 1 factor (diagnosis) with three levels (e.g control, diag1, diag2) in order to compare cortical thickness in these diagnostic groups. I am coming across two main errors; 1. The first one I get upon clicking "analyze" in the q

[Freesurfer] GLM analysis freeview error

Hello, I have encountered a silly error message I'm hoping someone can help me with. I've been following the GLM analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis) and have managed to go through all the steps; however I am now having issues visualizing my re

[Freesurfer] cortical thickness analysis

Hi freesurfer experts, I have a question I was hoping someone could help me with; I am currently analysing the cortical thickness of two subject populations (patient and control) using the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng). However, wh

[Freesurfer] extracting pvalues

Hi FreeSurfer experts, Is there a way to extract significant pvalues from sig.mgh files (Obtained from the GroupAnalysisDng tutorial)? I've looked online but having trouble. Somehow mris_covert isn't working. Thanks! Gabriella ___ Freesurfer mailing

[Freesurfer] group analysis question

Hi FS experts, I sent a similar question to this last week but I never got a response. Any ideas would be very much appreciated! I have gone through the Group Analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysisDng) and am trying to find a way to extract uncorr

[Freesurfer] cluster colors

Hi FS experts, I had a quick question I was hoping someone could help me with; I used the group analysis tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis_tktools) to analyse two groups of subjects. I ran the mri_glmfit command, as well as the clusterwise correction

Re: [Freesurfer] cluster colors

colors I don't think I understand. What files are you visualizing? What is your command to visualize? On 2/18/15 3:42 PM, Hirsch, Gabriella wrote: Hi FS experts, I had a quick question I was hoping someone could help me with; I used the group analysis tutorial (https://surfer.nmr.mgh

Re: [Freesurfer] tksurfer overlay threshold

5 03:21 PM, Hirsch, Gabriella wrote: > Hi Fs experts, > > I had a quick question about settings thresholds of surface overlays > in Tksurfer. I am currently generating images of the thickness, volume > and surface area of individual subjects, and would like to know if > there are

Re: [Freesurfer] tksurfer overlay threshold

e(min, mid,max) which will compute the thresholds based on the histogram of values On Tue, 3 Mar 2015, Douglas N Greve wrote: > > I'm not sure what you mean. optimal in what sense? > doug > > On 03/03/2015 03:21 PM, Hirsch, Gabriella wrote: >> Hi Fs experts, >> >

Re: [Freesurfer] tksurfer overlay threshold

ey set the threshold so that 92% of the values are not displayed, and the color scale saturates at the 99 percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Thanks Bruce! > > I tried using the command: > > sclv_set_current_threshold_from_percentile > > The t

Re: [Freesurfer] tksurfer overlay threshold

bly too old On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Hi Bruce, > > I tried using the command set_threshold_from_percentile as a tcl script but I > got the following error: > > tksurfer: run tcl script: threshold.tcl > invalid command name "set_threshold_from_percen

Re: [Freesurfer] tksurfer overlay threshold

hreshold_from_percentile" not > "set_threshold_from_percentile" as you have in your email. > > -Zeke > > On 03/04/2015 11:07 AM, Bruce Fischl wrote: >> you would need to include parameters, but that doesn't explain your error. >> What version of tksurfer are you usin

Re: [Freesurfer] tksurfer overlay threshold

: threshold.tcl invalid command name "set_current_threshold_from_percentile"% Any thoughts would be greatly appreciated! Thank you. Gabriella From: Z K [zkauf...@nmr.mgh.harvard.edu] Sent: Wednesday, March 04, 2015 2:32 PM To: Hirsch, Gabriella S

Re: [Freesurfer] tksurfer overlay threshold

: sclv_set_current_threshold_from_percentile cheers Bruce On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > Hi Bruce, > > I have been in touch with Zeke, who was kind enough to help me update my > version of Tksurfer. Unfortunately, this has not solved my problem (see > below). > > I

Re: [Freesurfer] tksurfer overlay threshold

: [Freesurfer] tksurfer overlay threshold you need it to be: % sclv_set_current_threshold_from_percentile .7 .8 .9 or something like taht On Wed, 4 Mar 2015, Hirsch, Gabriella wrote: > OK, I tried that, and it does load however I get this message in the terminal: > > tksurfer: run t

[Freesurfer] glmfit-sim question

Hi FS experts, I had a quick question about glmfit-sim in monte carlo. I have followed the FS wiki by using the following command to correct for multiple comparisons separately on both hemispheres: mri_glmfit-sim \ --glmdir_?h.xxx.glmdir \ --sim mc-z 1 1.3 mc-z.absolute \ --sim-sign abs --c

[Freesurfer] interpreting glmfit-sim results

Hi FS experts, I had a couple quick questions about interpreting glmfit-sim results. For context, I'm interesting in analyzing surface-based morphology differences (cortical thickness, volume, surface area) between two groups. I ran a simple t-test contrast (1 -1) using glmfit on two groups (co

[Freesurfer] interpreting glmfit-sim results

Hello FS experts, I submitted this question yesterday but never heard back. Any thoughts? Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Monday, May 04, 2015 3:03 PM To: freesurfer

[Freesurfer] qdec table loading error

Hi FS experts, I'm having a really tough time trying to get my qdec.table.dat table to load into the qdec GUI. I have gone through the wiki painstakingly and have no idea why it's giving me this error message: Reading /usr/local/freesurfer/tktools/tkUtils.tcl Using /usr/local/freesurfer/lib/tc

Re: [Freesurfer] qdec table loading error

Scratch that - I simply changed the level name from "blind" to "EB" and it worked. Clearly qdec didn't like my naming assignments. Thanks anyway! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch,

[Freesurfer] demean values in QDEC

Hi FS experts, I had a quick silly question about QDEC - I'm trying to run a group morphometry analysis of cortical volume between two groups (patient and control). I want to use ICV as a nuisance covariate and noticed you need to demean the ICV values in order for QDEC to work. My question is:

[Freesurfer] ICV correction for volume analysis

Hi FreeSurfer experts, I have a couple quick questions I'm hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical

[Freesurfer] FW: correcting for brain size

HI FS experts, I haven't heard back and am still wrestling with these questions. Any takers? I'd really appreciate any thoughts at all if possible. Thanks, Gabriella From: Hirsch, Gabriella Sent: Wednesday, May 20, 2015 3:55 PM To: freesurfer@nmr.mgh.harvard.edu Subject: ICV corr

Re: [Freesurfer] FW: correcting for brain size

s were diminished to nothing. Hope this helps. -David Vazquez PhD candidate in Cognitive Neuroscience University of California, Riverside NSF GRFP fellow On Fri, May 22, 2015 at 6:16 AM Hirsch, Gabriella mailto:gabriella_hir...@meei.harvard.edu>> wrote: HI FS experts, I haven’t heard back a

Re: [Freesurfer] FW: correcting for brain size

[gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 3:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, sorry for the delay On 05/22/2015 09:15 AM, Hirsch, Gabriella wrote: > > HI FS experts, > > I haven’t heard back and a

Re: [Freesurfer] FW: correcting for brain size

: [Freesurfer] FW: correcting for brain size Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: > Thanks for the response, Doug! > > Yes, here is the error message I get when I try to keep one measure (e.g.

Re: [Freesurfer] FW: correcting for brain size

:30 PM, Hirsch, Gabriella wrote: > Sure thing, see attached. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wednesday, May 27,

Re: [Freesurfer] FW: correcting for brain size

c/Untitled/y.mgh On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: > Sure. > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Wed

Re: [Freesurfer] FW: correcting for brain size

thout your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: > Done. I wasn't sure if I had to put an email address for the recipient so I > put yours. Let me know if you figure it out! :) Thanks so much. >

Re: [Freesurfer] FW: correcting for brain size

urfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Wednesday, May 27, 2015 6:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size There should be one in aseg.stats. On 05/27/2015 05:45 PM, Hirsch, Gabriella wrote: > Yes, i

Re: [Freesurfer] FW: correcting for brain size

al for the hemi On 05/28/2015 09:12 AM, Hirsch, Gabriella wrote: > That's what I thought but it doesn't seem to be there; I only have the > following: > > BrainSegVol > BrainSegVolNotVent > BrainSegVolNotVentSurf > lhCortexVol > rhCortexVol > CortexVol &

Re: [Freesurfer] FW: correcting for brain size

Douglas N Greve Sent: Thursday, May 28, 2015 2:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size isn't that what you are looking for? On 05/28/2015 02:05 PM, Hirsch, Gabriella wrote: > Hmm, I tried looking and all I can find is total wm surface

[Freesurfer] reg-feat2anat update

Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in FSL in Freesurfer using reg-feat2anat (http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem to be having the same problem as the person in this thread:

[Freesurfer] FW: reg-feat2anat update

-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Monday, June 22, 2015 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] reg-feat2anat update Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in F

[Freesurfer] feat statistics on surface

a new version in response to a user about a year ago, but this seems to have been deleted/moved: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat Does someone know where I can update to this new version? Thank you! Gabriella From: Hirsch, Gabriella Sent: Monday, June

[Freesurfer] create ROI from label

Hi all, I'm trying to generate an ROI mask from the Freesurfer label lh.MT.label of a specific subject. I've browsed the documentation and the archives and it seems the best command to use is mri_label2vol. However, I can only seem to produce the "outline" of the label, if that makes sense (as

Re: [Freesurfer] create ROI from label

behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Tuesday, September 08, 2015 1:10 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] create ROI from label Try it with --fill-ribbon On 09/08/2015 11:01 AM, Hirsch, Gabriella wrote: > Hi all, > > I'm trying to g

Re: [Freesurfer] create ROI from label

r 08, 2015 2:35 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] create ROI from label try this version ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol On 09/08/2015 02:30 PM, Hirsch, Gabriella wrote: > Thanks Doug - I tried adding it but got an error:

[Freesurfer] qdec analysis with ICV

Hi Freesurfer Experts, I am hoping someone can help me solve this error I'm experiencing while conducting a simple qdec analysis. I have 4 subjects (3 vs 1) that I am trying to analyze for volume differences using a demeaned ICV as a nuisance factor (see attached fsgd file - note I changed the

Re: [Freesurfer] qdec analysis with ICV

Thanks for the suggestion David. I tried it but I still got the same error :/ Gabriella From: David Vazquez [mailto:dvazq...@ucr.edu] Sent: Friday, November 13, 2015 12:36 PM To: Hirsch, Gabriella Subject: Re: [Freesurfer] qdec analysis with ICV Hi Gabriella. I'm not an expert, but I&#

Re: [Freesurfer] qdec analysis with ICV

tract the mean value from each individual value). This has worked for me to bypass this error. -Andrew From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Hirsch, Gabriella" mailto:gabriella_hir...@meei.harvard.edu>> Reply-To: "freesurfer@nmr.m

Re: [Freesurfer] qdec analysis with ICV

oup analysis but you only have 1 subject in group B. There is no way to estimate the variance in the measure if there is only one subject in the group. -Andrew From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Hirsch, Gabriella" mailto:gabriella_hir...@mee

[Freesurfer] modify QDEC smoothing options

Hey Freesurfer experts, I had a quick question. Is there any way to modify QDEC in such a way to have other options other than 0, 5, 10, 15, 20 etc, for smoothing? I know I would also have to -qcache the data for the desired smoothing too but I was wondering if anyone had done this before? Any

[Freesurfer] fMRI activation color inversion

Hi FreeSurfer experts, I recently ran a simple fMRI analysis in FSL and now generating images of the activation in freesurfer using reg-feat2anat to register the functional activation to the freesurfer recon-all files, and generating the images using tksurfer: tksurfer pilot_3 lh inflated -ann

Re: [Freesurfer] fMRI activation color inversion

-fminmax option which is easier to explain. -fminmax 2 5 means that the threshold is set to 2 and that at 5 the color will saturate. doug On 01/11/2016 12:18 PM, Hirsch, Gabriella wrote: > Hi FreeSurfer experts, > > I recently ran a simple fMRI analysis in FSL and now generating images

Re: [Freesurfer] fMRI activation color inversion

inversion no, it is a matter of taste. Note that 2 is the threshold. If you are looking at sig maps, then the threshold may be important. The p-value threshold is 10^-fthresh On 01/11/2016 02:19 PM, Hirsch, Gabriella wrote: > Thanks Doug! This is very good to know. Is there a ratio

[Freesurfer] freeview error

Hi, I am trying to view surfaces in 3D using Freeview on my own subject data via this command (replacing the subject name); freeview -f good_output/surf/lh.pial:annot=aparc.annot:name=pial_aparc:visible=0 \ good_output/surf/lh.inflated:overlay=lh.thickness:overlay_threshold=0.1,3::name=inflate