Re: [Freesurfer] ROI Analysis

That basically looks right. One thing to note  is that you are sampling onto the average surface (fsaverage); this is not really doing surface-based analysis, it will be about the same as registering you individual subject to the mni152, then sampling your ROI atlas onto the individual subject'

[Freesurfer] ROI Analysis

External Email - Use Caution Hello FreeSurfer Community! I previously asked a question about volume quantification using an external atlas (in fact, there are 20 brain masks corresponding to the regions of interest). I managed to perform the quantification with the following comma

[Freesurfer] ROI analysis, S1, face area

External Email - Use Caution Dear FreeSurfer Team, I would like to do a ROI analysis focusing on the primary somatosensory cortex (S1) using Freesurfer and see the potential alterations after a (behavioral) treatment . I am wondering how I can do that? First, I picked and looked a

Re: [Freesurfer] ROI Correlations

External Email - Use Caution Thanks, I will let you know if I can make it work. On Jan 26, 2021, at 8:25 AM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: The only thing I have that I think will do what you want is a matlab script (annotval2surfoverlay.m, attached); c

Re: [Freesurfer] ROI Correlations

The only thing I have that I think will do what you want is a matlab script (annotval2surfoverlay.m, attached); copy it to $FREESURFER/matlab There is documentation in the file on how to run it. Can you look at that and see if you can make it work? On 1/26/2021 9:39 AM, Swanson,Clayton wrote:

Re: [Freesurfer] ROI Correlations

External Email - Use Caution Hi Doug, Thanks for getting back to me and sorry for not being more clear. I am trying to associate TMS related inhibitory measures to the left pre- and paracentral gyrus thickness for two different groups (healthy, MS). Additionally, I am intereste

Re: [Freesurfer] ROI Correlations

Sorry, I don't know what you mean. Can you elaborate? On 1/18/2021 11:47 AM, Swanson,Clayton wrote: External Email - Use Caution Hi Freesurfer Folks, I am wondering if it is possible to perform an ROI correlation which can then be viewed on the brain similar to whole brain GLM analysi

[Freesurfer] ROI Correlations

External Email - Use Caution Hi Freesurfer Folks, I am wondering if it is possible to perform an ROI correlation which can then be viewed on the brain similar to whole brain GLM analysis in Freeview. If so, how would I go about performing this type of operation as to specify tha

Re: [Freesurfer] ROI-wide cortical thickness for each network !

Try something like mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.yeo.stats -b -a ../label/lh.yeo.annot -c ../label/yeo.annot.ctab 1040 lh white Assuming that your yeo atlas is in $SUBJECTS_DIR/$subject/label/lh.yeo.annot On 7/15/2020 2:05 PM, Martin Juneja

Re: [Freesurfer] ROI-wide cortical thickness for each network !

External Email - Use Caution Dear Doug, Thanks for your response ! Yes, I have Yeo atlas in the individual space, and recon-all.log has the following command: mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.aparc.stats -b -a ../label/lh.aparc.anno

Re: [Freesurfer] ROI-wide cortical thickness for each network !

If you have the Yeo atlas in the individual space, you can use mris_anatomical_stats to compute stats the same as in the Desikan atlas. Look in recon-all.log for the command line and customize it as needed On 7/14/2020 5:00 PM, Martin Juneja wrote: External Email - Use Caution Hi e

[Freesurfer] ROI-wide cortical thickness for each network !

External Email - Use Caution Hi experts, I extracted network-wise cortical measures (i.e., 7 cortical thickness values for 7 networks for Yeo atlas). I was wondering if there is a way to get the cortical thickness of each ROI within each of these networks e.g., cortical thickness

Re: [Freesurfer] ROI Analysis in a given label with Functional Constraint in FSFAST

External Email - Use Caution Thank you for your response.  I have 2 questions.1. I want to extract a binary ROI after group analysis with the command:mri_binarize --i lh.sig.nii.gz --min 9.13 --mask lh.V3A.nii.gz --o lh.ROI.nii.gzfreeview -f $SUBJECTS_DIR/fsaverag

Re: [Freesurfer] ROI Analysis in a given label with Functional Constraint in FSFAST

Is the hV5+MT label already a binary volume in the FS conformed 1mm space (ie, same space as orig.mgz)? And what do you mean by "constrained"? On 2/13/2020 11:04 AM, Star Xi wrote: External Email - Use Caution FS experts, Commonly, I can use mri_vol2vol -> mri_segstats to extract anat

[Freesurfer] ROI Analysis in a given label with Functional Constraint in FSFAST

External Email - Use Caution FS experts,Commonly, I can use mri_vol2vol -> mri_segstats to extract anatomical ROI from aparc or aseg template.However, now I want to extract the average percent signal change in the hV5+/MT by constrained  positive functiona

Re: [Freesurfer] ROI analysis with manually created labels

Hi Yuanyuan this is really more of a batch processing/shell scripting question than a FreeSurfer one. Something like (in tcsh) set SUBJECTS = (N001 N002...) foreach s ($SUBJECTS) mris_anatomical_stats -l lh.precentral.label -t lh.thickness -b \ -f $s/stats/lh.precentra

[Freesurfer] ROI analysis with manually created labels

External Email - Use Caution Dear FreeSurfer developers, I used Freesurfer QDEC for group comparisons and identified clusters with significance cortical thickness between the Patient group and the Control group. Then I created several ROIs manually, saved them as labels, and ma

Re: [Freesurfer] ROI mask extraction from asec and apark

Look here, example #9 http://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems On 3/14/19 5:01 AM, Tim Hahn wrote: > External Email - Use Caution > > Dear Freesurfer experts, > > as far as I understand, Freesurfer employs the Desikan-Killiany Atlas > (by default) to compute the various

[Freesurfer] ROI mask extraction from asec and apark

External Email - Use Caution Dear Freesurfer experts, as far as I understand, Freesurfer employs the Desikan-Killiany Atlas (by default) to compute the various parameters based on the aseg and aparc files. For my analysis, I now need the Desikan-Killiany Atlas ROI mask(s) (cort

[Freesurfer] ROI Analysis

External Email - Use CautionHi everybody,   after finishing my group analysis I am currently trying to run a ROI analysis. However I have some problems/general questions. I am trying to draw a ROI on fsaverage in order to use the mri_label2label command afterwards. I opened Fre

Re: [Freesurfer] ROI extraction using functional masks

External Email - Use Caution Hi Doug, I apologise for the time I left this question unanswered… I have done some work on the issue, and discovered that the orientation was wrong (eg left ROI was on the right side), but this did not appear on step 2. Anyway, this is now fixed.

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

Behalf Of Yendiki, Anastasia Sent: Thursday, February 15, 2018 12:52 PM To: Freesurfer support list Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Hi Donald - If you have recent dicoms from a standard manufacturer's sequence, then mri_convert should be able to read t

Re: [Freesurfer] ROI extraction using functional masks

At what step is the failure happening? Do the masks look ok on the surface? On 02/12/2018 08:06 PM, Yann Quidé wrote: > Dear FS experts, > > I am trying to extract values for cortical thickness, surface area and > volumes, from different functional ROIs. These cortical ROIs have been > defined

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

ort list Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Dear a.y. Thanks for getting back. I’ve set the wheels in motion to run tracula on the control scans that we have. I found your notes in the diffusion_tutorial download for grabbing the bval and bvecs from each DTI s

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

esday, February 14, 2018 6:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI That's correct, you'd have to run TRACULA on a subject to get those files. They're computed from those 33 subjects, but you can't g

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

er, Donald N. Sent: Wednesday, February 14, 2018 5:19:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Thank you very much for getting back on this so promptly, a.y. If I understand correctly, I think it’s the information in the *

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

arvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Yendiki, Anastasia Sent: Wednesday, February 14, 2018 4:34 PM To: Freesurfer support list Subject: Re: [Freesurfer] List needed: pathway <==> freesurfer ROI Hi Donald - TRACULA doesn't use deterministic ROIs, instead it a

Re: [Freesurfer] List needed: pathway <==> freesurfer ROI

ist mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Wednesday, February 14, 2018 at 10:19 AM To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] List needed: pathway <==> freesurfer ROI Dear L

[Freesurfer] List needed: pathway <==> freesurfer ROI

Dear List, I need a list of Freesurfer ROIs which are typical endpoints for each standard pathway used in tracula. I think this information is likely included in the default tracula atlas which I have been unable to find although I do not need spatial coordinates but rather just the list of ROI

[Freesurfer] ROI extraction using functional masks

Dear FS experts, I am trying to extract values for cortical thickness, surface area and volumes, from different functional ROIs. These cortical ROIs have been defined using SPM tools, and are in .nii format. My scans have been processed using FS v5.3. Although the conversion seems to go well, t

Re: [Freesurfer] ROI statistics and median values

I don't think we have anything. You can do it in matlab, eg aseg = MRIread('aseg.mgz'); vol = MRIread('vol.nii.gz'); ind = find(aseg.vol==17); % left hippo median(vol.vol(ind)) On 1/12/18 10:42 AM, Helen Beaumont wrote: > I can use mri_segstats to get mean and std dev for values within a > s

[Freesurfer] ROI statistics and median values

I can use mri_segstats to get mean and std dev for values within a segmented image. Is there any way I can get median values? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The i

Re: [Freesurfer] ROI labeling?

7 4:55 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ROI labeling? > > what do you mean by an average of the mask? Such an average would not be > binary. > > > On 08/03/2017 04:30 PM, Sadie Marvel wrote: >> And what if I wanted to compute just one ROI

Re: [Freesurfer] ROI labeling?

l ROI masks? > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: Thursday, August 3, 2017 4:15 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ROI labeling? > > If you are just going to use them

Re: [Freesurfer] ROI labeling?

masks? > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Douglas N Greve > > Sent: Thursday, August 3, 2017 4:15 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] ROI labeling? > > If you are just going to use them as a mask for mri

Re: [Freesurfer] ROI labeling?

: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ROI labeling? If you are just going to use them as a mask for mri_glmfit, then you can just pass it as --mask or --label, no need to map it back to the individual (which you could do with mri_surf2surf) On 08/03/2017 04:08 PM, Sadie Marvel wrote

Re: [Freesurfer] ROI labeling?

If you are just going to use them as a mask for mri_glmfit, then you can just pass it as --mask or --label, no need to map it back to the individual (which you could do with mri_surf2surf) On 08/03/2017 04:08 PM, Sadie Marvel wrote: > Hi again Freesurfers, > > I am doing a surface based ROI ana

[Freesurfer] ROI labeling?

Hi again Freesurfers, I am doing a surface based ROI analysis where for each subject, isomorphic ROIs of 300 vertices (centered around peak functional activations) were found on the fsaverage surface space. I was wondering if I should register these masks that I have created back to each subjec

Re: [Freesurfer] ROI analyses using SPM AAL ROIs

not sure, a pointer to the page would make it easier. probably it is the T1 image of the mni152 that is distributed with FSL and SPM On 7/3/17 1:33 AM, M Janani wrote: Hi Team, Currently I’m working on ROI analyses. I saw one article related to VolumeROICorticalThickness in

[Freesurfer] ROI analyses using SPM AAL ROIs

Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from SPM.

[Freesurfer] ROI analyses using SPM AAL ROIs

Hi Team, Currently I'm working on ROI analyses. I saw one article related to VolumeROICorticalThickness in Free surfer wiki. Could anyone please tell me what is the anatomical file(TT_avg152T1.nii) they are referring to? I took AAL ROIs from SPM.

Re: [Freesurfer] ROI seed size

these are good questions without good answers. It is hard to compare surface-based vs volume-based. The surface-based may be smaller, but it will only include gray matter whereas a volume-based sphere will be bigger but will include WM and CSF. If you're voxel size is small, then 3mm radius mig

Re: [Freesurfer] ROI seed size

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] ROI seed size

Hi Erik what are you using the seed for? A 3mm radius is a relatively small spot on the surface cheers Bruce On Mon, 3 Apr 2017, ERIK JAHNER wrote: What is the appropriate size for a surface based seed? I am referencing a study with volumetric based seeds with spheres with a radius of 3m

[Freesurfer] ROI seed size

What is the appropriate size for a surface based seed? I am referencing a study with volumetric based seeds with spheres with a radius of 3mm (in fMRI data). I would like to do a similar study using surface based representations. In a volumetric based analysis folding may actually increase the

Re: [Freesurfer] ROI analysis - smoothing

no, that is fine too On 03/15/2017 04:49 PM, Mihaela Stefan wrote: > I was thinking to use lme_mass_FDR2 to correct for multiple > comparisons. Is there a reason not to use it in this case? > > Thank you! > Mihaela > > On Wed, Mar 15, 2017 at 3:55 PM, Douglas N Greve > mailto:gr...@nmr.mgh.harv

Re: [Freesurfer] ROI analysis - smoothing

I was thinking to use lme_mass_FDR2 to correct for multiple comparisons. Is there a reason not to use it in this case? Thank you! Mihaela On Wed, Mar 15, 2017 at 3:55 PM, Douglas N Greve wrote: > No, there is not. You can do it that way if you want to. The problem is > that you then end up with

Re: [Freesurfer] ROI analysis - smoothing

No, there is not. You can do it that way if you want to. The problem is that you then end up with stuff outside of the ROI smoothing into the ROI. Also note that either way, you will need to generate new tables for correction of multiple comparisons (use use permutation) On 03/15/2017 03:52 PM

Re: [Freesurfer] ROI analysis - smoothing

Is there a way or reference this smoothing detail in a paper? There are people who believe that the soothing should be done at the whole brain level and then apply the mask (--label), during the GLM analysis. Thanks again! Mihaela On Wed, Mar 15, 2017 at 3:12 PM, Douglas N Greve wrote: > yes, t

Re: [Freesurfer] ROI analysis - smoothing

yes, that is the right way to do it On 03/15/2017 01:18 PM, Mihaela Stefan wrote: > Hello FreeSurfers, > > I would like to run a group analysis on cortical thickness using > existing Desikan labels. > > When I run the command for smoothing, should I replace *--cortex* with > *--label-trg*? In o

[Freesurfer] ROI analysis - smoothing

Hello FreeSurfers, I would like to run a group analysis on cortical thickness using existing Desikan labels. When I run the command for smoothing, should I replace *--cortex* with *--label-trg*? In other words, for ROI analysis, should we smooth *only* the target mask? mri_surf2surf --hemi lh \

Re: [Freesurfer] ROI with precise coordinates

.edu> de la part de Dr. M. Shahid > *Envoyé :* mardi 17 janvier 2017 14:44 > *À :* Freesurfer support list > *Objet :* Re: [Freesurfer] ROI with precise coordinates > > Hi, > > Yes you can use fslmaths and Ants ImageMath to make an ROI from the given > mni coordinates.

Re: [Freesurfer] ROI with precise coordinates

d.edu de la part de Dr. M. Shahid Envoyé : mardi 17 janvier 2017 14:44 À : Freesurfer support list Objet : Re: [Freesurfer] ROI with precise coordinates Hi, Yes you can use fslmaths and Ants ImageMath to make an ROI from the given mni coordinates. The command is like fslmaths MNI_T1...gz -

Re: [Freesurfer] Roi parcellation

can you please include the entire correspondence. We get a lot of emails and it's hard for us to keep track otherwise thanks Bruce On Wed, 18 Jan 2017, Aya Kabbara wrote: > > Thank you.. > > Actually, I realized that using tksurfer I can do a manual parcellation. > However, I need an automati

Re: [Freesurfer] Roi parcellation

Hello, Two options I can think of--develop your own atlas (time consuming), or apply the Lausanne atlas parcellation, and combine the smaller ROIs to get the ones you want. See this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2016-February/043869.html https://github.com/m

[Freesurfer] Roi parcellation

Thank you.. Actually, I realized that using tksurfer I can do a manual parcellation. However, I need an automatic parcellation. Is there a way? Get Outlook for Android ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu htt

Re: [Freesurfer] ROI with precise coordinates

Hi, Yes you can use fslmaths and Ants ImageMath to make an ROI from the given mni coordinates. The command is like fslmaths MNI_T1...gz -mul 0 -add 1 roi xmin xsize ymin ysize zmin zsize tmin tsize ROI_name. For a box of 10mm , you can use fslmaths kernel boxv... or for a sphere you can use Image

Re: [Freesurfer] ROI with precise coordinates

janvier 2017 15:46 À : freesurfer@nmr.mgh.harvard.edu Objet : [Freesurfer] ROI with precise coordinates Dear all, I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars

[Freesurfer] ROI with precise coordinates

Dear all, I would like to know how to make an ROI an FreeSurfer/QDEC with precise coordinates. More precisely, I want an ROI called IFC consisting of combined pars opercularis and pars triangularis and with a box of 10 x 10 x 10 mm size, centered at MNI coordinates 10,-15,-5. Does a comman

Re: [Freesurfer] ROI NumVert

You should be able to apply the mris_preproc command on the xhemi page https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi substituting your average subject for fsaverage_sym On 11/04/2016 10:41 AM, Daya P wrote: > I went to the shell script and changed the input for aparc+aseg and > aseg. and ma

Re: [Freesurfer] ROI NumVert

I went to the shell script and changed the input for aparc+aseg and aseg. and managed to make it work. My other question is that now that I have it running, after it is done I would like to run a vertex wise analysis. Is there a tutorial/help or command that I should apply to do asymmetry anal

Re: [Freesurfer] ROI NumVert

Try adding --zilles --reg It is a hack, but it might just work On 11/04/2016 07:34 AM, daianapu...@gmail.com wrote: > > Hi, > > Thank you for your reply, when I run xhemireg I get an error for > cannot find aseg. is there any way to avoid that? in the way there is > a noaseg flag for other co

Re: [Freesurfer] ROI NumVert

Hi, Thank you for your reply, when I run xhemireg I get an error for cannot find aseg. is there any way to avoid that?  in the way there is a noaseg flag for other commmands. I built a cortical Atlas and dont have subcortical labels Thank you , Daiana Daiana Pur On Wed, Nov 2, 2016 at

Re: [Freesurfer] ROI NumVert

oh, sorry, it does assume that you have pbsubmit, I had forgotten that. You can actually follow the instructions for building your own atlas at the bottom of the xhemi web page http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi This does the same thing as make_folding_atlas. It takes a long time if

Re: [Freesurfer] ROI NumVert

Hi, When i try running make_folding_atlas I get xhemireg Trout2016 Wed Nov 2 13:11:23 EDT 2016 #@# xhemireg --s Trout2016 pbsubmit: Command not found. Launched 9 xhemireg processes #%# Waiting for 9 xhemireg processes Wed Nov 2 13:11:33 EDT 2016 #%# Waiting for 9 xhemireg processes Wed Nov 2

Re: [Freesurfer] ROI NumVert

On 11/01/2016 05:58 PM, Daya P wrote: > Hi, > > I have gotten the lh and rh ROIs stats with mris_anatomical_stats > before, is there any statistical tests in particular that you > recommend for asymmetry? What I have done is a two-way anova and > paired t-test with Bonferroni correction. Would

Re: [Freesurfer] ROI NumVert

Hi, I have gotten the lh and rh ROIs stats with mris_anatomical_stats before, is there any statistical tests in particular that you recommend for asymmetry? What I have done is a two-way anova and paired t-test with Bonferroni correction. Would like to hear your opinion on that. Also, I would be

Re: [Freesurfer] ROI NumVert

You can certainly get the lh and rh ROI stats in table form and then do an asymmetry analysis. Or you can use the xhemi stream to do a vertex-wise analysis. the difference is the difference between ROI and map-based analysis On 11/01/2016 03:47 PM, Daya P wrote: > Thank you a lot! > > I will t

Re: [Freesurfer] ROI NumVert

Thank you a lot! I will try this. I had another question regarding statistical analysis for asymmetry. I have seen several papers that take the measures that come from freesurfer (i.e. cortical thickness of auditory cortex), and use MATLAB or SPSS to run statistical tests. I am looking at 13 regi

Re: [Freesurfer] ROI NumVert

I've written a script that will come out with version 6, but I've put it here https://gate.nmr.mgh.harvard.edu/safelinks/greve/make_folding_atlas I think it should work in 5.3, but I'm not sure. If not, you can download the dev version and make the atlas using that. Run it with --help to get i

Re: [Freesurfer] ROI NumVert

Hi Doug, I needed to make a registration template and an cortical atlas because I am trying to measure cortical thickness, GM and surface area on cat brains. What would be the necessary changes? Would it be possible (and appropriate) to use just mris_left_right_register instead? Daiana On Fri,

Re: [Freesurfer] ROI NumVert

A difference of 10 out of 500 or 1000 does not both me at all. Why do you need to create your own atlas? It is doable for the cross hemi stuff, it is just difficult. On 10/26/16 10:16 AM, Daya P wrote: Thank you for your help! I created a registration template and atlas from scratch could I

Re: [Freesurfer] ROI NumVert

Thank you for your help! I created a registration template and atlas from scratch could I input that in the interhemispheric registration analysis? The ROIs for the diffrerent regions per hemisphere are 50-100 vertices On Oct 24, 2016 5:03 PM, "Douglas N Greve" wrote: > It would depend on how b

Re: [Freesurfer] ROI NumVert

It would depend on how big the ROI is to begin with. Do you know that we have our own interhemispheric analysis that might be better for this? Check out http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 10/24/2016 12:33 PM, Daya P wrote: > Hi Bruce, > > I drew ROIs on an initial subject and th

Re: [Freesurfer] ROI NumVert

Hi Bruce, I drew ROIs on an initial subject and then after registering all other subjects to the initial one, used mri_label2label to map the ROIs from the initial subject to subsequent ones. I am interested in looking at asymmetry between left and right regions. I had two concerns, one that the

Re: [Freesurfer] ROI NumVert

Hi Daiana yes, that is to be expected given the nonlinear nature of the cross-subject registration. It shouldn't bias things, although you'll need to give us more details if you want a more definitive answer. cheers Bruce On Mon, 24 Oct 2016, Daya P wrote: Hi All, My question is about us

[Freesurfer] ROI NumVert

Hi All, My question is about using mri_label2label. When mapping the labels from one subject to another the number of vertices of each ROI is different. Is that something to be expected? How much of a difference does a number of vertices of 50 compare to 40 have on measures like thickness, grey m

[Freesurfer] ROI-based laminar BOLD analysis

Dear FreeSurfer team, My name is Alex Wilks, an undergrad in the fMRI lab at the University of Michigan. We are trying to learn the ropes of FreeSurfer so that we may be able to perform high resolution fMRI analysis across multiple cortical layers. So far, I have understood how to generate inte

Re: [Freesurfer] roi mask?

yes, they are based on different atlases. You can look at the original papers (Rahul Desikan's is one and Christophe Destriuex's is the other) to see the differences. Or you can load the various .annot files in freeview on the inflated surface to see them visually cheers Bruce On Fri, 27 May 2

Re: [Freesurfer] roi mask?

Hi Bruce, Thanks for the fast response! I indeed found them in other stats files. What is the difference between these files? I assume they are based on different atlases? I saw that there are some slight differences between the numbers in different files for the same structures, so how do I know

Re: [Freesurfer] roi mask?

it depends what they are. You can look in the other stats files to see if they are there (we include a couple of cortical parcellations). If they aren't, you can draw them yourself on fsaverage and map them to all your subjects using our spherical transform cheers Bruce On Fri, 27 May 2016, Ma

Re: [Freesurfer] roi mask?

Hi Bruce, Thanks, that indeed includes most of the roi's I want to include. What if there are some area's that are not in that list? Is there a way of adding areas? Best, Marja On Fri, May 27, 2016 at 10:26 PM, Bruce Fischl wrote: > Hi Marja > > what ROI do you mean? We generate lots of them,

Re: [Freesurfer] roi mask?

Hi Marja what ROI do you mean? We generate lots of them, and tabulate the thickness within each one. Look for example in id>/stats/aparc.stats cheers Bruce On Fri, 27 May 2016, Marja Caverlé wrote: Hi all, So I ran a recon-all -all on one of my subjects, and it completed without errors (acc

[Freesurfer] roi mask?

Hi all, So I ran a recon-all -all on one of my subjects, and it completed without errors (according to the log). Now I would like to get cortical thickness numbers from this subject, but when I open the tutorial regarding this, it says it assumes that you already have a roi mask and a T1 in the sa

[Freesurfer] ROI within subject

Dear. Freesurfer experts. Hi. How are you? I have a question about making ROI. This might be a naive question, but any input would be greatly appreciated. I preprocessed scans per run, thus I have register.dof6.dat file inside all run epi directories. Then, I made ROIs per single subject based

Re: [Freesurfer] ROI

You'll have to run the interhemispheric analysis first. See https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi When that is finished, contact me again and I'll tell you how to transfer the labels On 11/09/2015 07:51 AM, UQAM wrote: > Hi > > I have created and saved labels for 2 regions in the ant

[Freesurfer] ROI

Hi I have created and saved labels for 2 regions in the anterior cingulate and corpus callosum in the left hemisphere and I would like to know if there is a way I can convert my .label files from the lh->rh without drawing them by hand in the other hemisphere. Thanks in advance, Best regards, Ge

Re: [Freesurfer] Freesurfer ROI

; > How do I next do the group comparison on the ROI? > > Many thanks again, > > Lena > > *From:*freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] *On Behalf Of *Bruce > Fischl > *Sent:* 04 September 2015 15:25 > *To:* Frees

Re: [Freesurfer] Freesurfer ROI

: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer ROI   Hi Lena Sure, but you will need to run all your subjects through recon-all first. The if the ROI is in MNI space you can use mri_label2label to map it to our group space fsaverage. Cheers Bruce On Sep 4, 2015, at 9:27 AM, Lim, Lena

Re: [Freesurfer] Freesurfer ROI

] On Behalf Of Bruce Fischl Sent: 04 September 2015 15:25 To: Freesurfer support list Subject: Re: [Freesurfer] Freesurfer ROI Hi Lena Sure, but you will need to run all your subjects through recon-all first. The if the ROI is in MNI space you can use mri_label2label to map it to our group space

Re: [Freesurfer] Freesurfer ROI

Hi Lena Sure, but you will need to run all your subjects through recon-all first. The if the ROI is in MNI space you can use mri_label2label to map it to our group space fsaverage. Cheers Bruce > On Sep 4, 2015, at 9:27 AM, Lim, Lena wrote: > > Sorry, I haven’t heard any replies so am re-post

Re: [Freesurfer] Freesurfer ROI

Sorry, I haven't heard any replies so am re-posting this again for help please: Dear Experts, I have 3 groups: A, PC, HC I did a VBM analysis in SPM and found group differences in grey matter volume in 2 clusters: 1) Bilateral pre-/SMA, left middle/superior frontal gryi 2) left inferior/middle

[Freesurfer] Freesurfer ROI

Dear Experts, I have 3 groups: A, PC, HC I did a VBM analysis in SPM and found group differences in grey matter volume in 2 clusters: 1) Bilateral pre-/SMA, left middle/superior frontal gryi 2) left inferior/middle temporal/fusiform/inferior/middle occipital gyri/superior/inferior posterior ce

Re: [Freesurfer] Multimodal Extraction of Freesurfer ROI Intensity Values

Try mri_segstats. Run with --help for more info and examples doug On 07/17/2015 02:01 PM, Lakhani, Bimal wrote: > Hello, > > To this point, I have been able to successfully register Myelin Water > Fraction (MWF) scans to Freesurfer Base Space in the longitudinal > pipeline (thank you for the hel

[Freesurfer] Multimodal Extraction of Freesurfer ROI Intensity Values

Hello, To this point, I have been able to successfully register Myelin Water Fraction (MWF) scans to Freesurfer Base Space in the longitudinal pipeline (thank you for the help with that!). What I would like to do next is use Freesurfer ROIs to automatically extract the mean intensity of the MW

[Freesurfer] ROI Analysis

Hello Freesurfer experts, I ran an analysis using mri_glmfit and a manually drawn label of the parietal lobe that was mapped to every subject and a tablefile was used as the dependent measure. The output is a negative log 10 p-value. I was curious if I could possibly view that in freeview on an fs

[Freesurfer] ROI

Dear FreeSurfer experts, I drew a label that crosses the cortical and subcortical boundary. But FreeSurfer still allows me to obtain statistics using this label for a given subject, for example, area, volume, and thickness. I am wondering if these statistics are valid since it crosses cortical

[Freesurfer] ROI analysis problem...

Hi Freesurfer community, I'm having a difficulty extracting signal from an ROI using funcroi-config and funcroi-table-sess. Every time I try to run the commands, I get the same error message: "ERROR: there is a vertex in the label that cannot be matched to the surface. This usually occurs when

Re: [Freesurfer] Freesurfer ROI analysis

t: Re: [Freesurfer] Freesurfer ROI analysis Hi Silas I'll leave the movement question for Martin Reuter who has been investigating this extensively. For your other question, one of the central focuses of our recent research has been in improving the sensitivity and reliability of longiudinal

Re: [Freesurfer] Freesurfer ROI analysis

f OFC grey matter thickness in the two groups; on and off medication (using freesurfer). Is Martin Reuther on vacation at the moment? Best, Silas Date: Fri, 25 Jul 2014 09:45:16 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer ROI analysi

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