Re: [Freesurfer] mri_segstats --avgwf output question

External Email - Use Caution It is going to list the cluster=0 value as the first value. cluster=0 are all the voxels not in a cluster. If you want to exclude this, just add --excludeid 0 On 8/10/2023 7:58 PM, Lara Foland-Ross wrote: External Email - Use Caution Hi

[Freesurfer] mri_segstats --avgwf output question

External Email - Use Caution Hi there, I'm running mri_segstats on a collection of clusters resulting from a statistical analysis. My command line usage is as follows:   mri_segstats --i lh.fwhm10.thickness.mgh --avgwf clusterAverages.txt --seg cache.th13abs.sig.ocn.mgh

Re: [Freesurfer] mri_segstats --sbTIVin

External Email - Use Caution Hmm, it does not look like that option was ever added (ie, that wiki page is incorrect). On 8/6/2023 8:13 AM, Woo-Suk Tae wrote: External Email - Use Caution Dear Freesurfer developer. According to the explanation in the *MailScanner has

[Freesurfer] mri_segstats --sbTIVin

External Email - Use Caution Dear Freesurfer developer. According to the explanation in the

Re: [Freesurfer] mri_segstats dimension mistach

:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing *Sent:* Wednesday, July 5, 2023 9:53 AM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] mri_segstats dimension mistach You don't often get email from yhuan...@mgh.harvard.edu. Learn why this is important

Re: [Freesurfer] mri_segstats dimension mistach

gh.harvard.edu Subject: [Freesurfer] mri_segstats dimension mistach External Email - Use Caution Hello, I'm trying to run the mri_segstats on different input volume. The input volume has the same dimensions as the original volume used to perform recon-all. However, when trying to use

Re: [Freesurfer] mri_segstats dimension mistach

...@nmr.mgh.harvard.edu On Behalf Of Fahad Hannan Sent: Monday, July 3, 2023 3:05 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_segstats dimension mistach External Email - Use Caution Hello, I'm trying to run the mri_segstats on different input volume. The input volume has the same

[Freesurfer] mri_segstats dimension mistach

External Email - Use Caution Hello, I'm trying to run the mri_segstats on different input volume. The input volume has the same dimensions as the original volume used to perform recon-all. However, when trying to use the following command: "mri_segstats --seg

Re: [Freesurfer] mri_segstats

You can pass it a --mul SCALE option to multiply the output by any scaling factor On 3/7/2023 1:16 PM, John Anderson wrote: External Email - Use Caution Dear Freesurfer community, Please forgive me for the basic nature of my question. I was wondering whether there is an argument that

[Freesurfer] mri_segstats

External Email - Use Caution Dear Freesurfer community, Please forgive me for the basic nature of my question. I was wondering whether there is an argument that can be included in mri_segstats to display the results in cubic centimeters (cm^3) instead of cubic millimeters (mm^3).

Re: [Freesurfer] mri_segstats question: --avgwf for cross hemisphere ROI

Hi Bram, there is not a way to do it with a single command. You could use the aparc+aseg, merge the two hemi labels into one, then run mri_segstats. If you want to stick with pure surface-based analysis, then you'd have to  run mri_segstats twice, then just compute a weighted mean of the two

[Freesurfer] mri_segstats question: --avgwf for cross hemisphere ROI

External Email - Use Caution Hello FreeSurfer Team, I've made a New Year's resolution to stop bothering Andrew Hoopes and instead send my questions to the FreeSurfer Mailing List. I would like to calculate a single average waveform for two surface labels on contralateral

Re: [Freesurfer] mri_segstats error:

half Of Brooklyn Wright Sent: Wednesday, January 4, 2023 9:17 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mri_segstats error: External Email - Use Caution Hello Freesurfer Developers, I am currently trying to perform reconstructions on 1mm^3 T1 data and am finding this error

[Freesurfer] mri_segstats error:

External Email - Use Caution Hello Freesurfer Developers, I am currently trying to perform reconstructions on 1mm^3 T1 data and am finding this error towards the end of the processing; \n mri brainvol _stats cor. 15 \n Segmentation fault Darwin UW-C02L2083DNMP 18.7.0 Darwin

Re: [Freesurfer] mri_segstats to report empty and non-empty segmentation

Try adding --empty On 4/12/2021 4:58 PM, miracle ozzoude wrote: External Email - Use Caution Hello Experts, I am using mri_segstats with the --ctab flag to extract dti and suvr values from a white matter hyperintensities parcellation. Running mri_segstats on the image and

[Freesurfer] mri_segstats to report empty and non-empty segmentation

External Email - Use Caution Hello Experts, I am using mri_segstats with the --ctab flag to extract dti and suvr values from a white matter hyperintensities parcellation. Running mri_segstats on the image and parcellation with --ctab only reports on non-empty segmentations. I

Re: [Freesurfer] mri_segstats question

External Email - Use Caution The WM was cropped out by applying a grey-matter mask in SPM, and I am trying to extract non-zero voxels with mri_segstats. Best, Renxi > On Nov 29, 2020, at 11:23 AM, Greve, Douglas N.,Ph.D. > wrote: > > I don't understand why WM was cropped

Re: [Freesurfer] mri_segstats question

what is your command line? On 11/29/2020 2:55 PM, RENXI LI wrote: > External Email - Use Caution > > The WM was cropped out by applying a grey-matter mask in SPM, and I am trying > to extract non-zero voxels with mri_segstats. > > Best, > Renxi > >> On Nov 29, 2020, at 11:23 AM, Greve,

Re: [Freesurfer] mri_segstats question

I don't understand why WM was cropped out. What command were you trying to use? On 11/18/2020 2:39 AM, RENXI LI wrote: > External Email - Use Caution > > Hi Freesurfer experts: > > I am trying to extract the mean-time series from the functional image using > mri_segstats. However, the

[Freesurfer] mri_segstats question

External Email - Use Caution Hi Freesurfer experts: I am trying to extract the mean-time series from the functional image using mri_segstats. However, the cerebral white matter signals were cropped out in my functional images, and the regions that I am trying to extract signal

Re: [Freesurfer] mri_segstats quetsion

Great. thanks Doug! Zahra (Mona) Nasiriavanaki, M.D. Postdoctoral Research Fellow Department of Psychiatry Massachusetts General Hospital 149 13th Street, 149-2615 Charlestown, MA, USA, 02129 On Sep 4, 2020, at 1:07 PM, Douglas N. Greve mailto:dgr...@mgh.harvard.edu>> wrote: I'm not entirely

Re: [Freesurfer] mri_segstats quetsion

I'm not entirely sure what those steps are trying to do. Extract out signal from voxels in thalamus that have a positive sig? You can do that with one call to mri_segstats. This page has an example: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultiModalFmriIndividual_freeview On

[Freesurfer] mri_segstats quetsion

Dear Freesurferers Hi I am trying to extract the BOLD signal values from a functional subcortical area. I did the below steps to make the functional thalamus ROI and then used the mri_segstats to extract the BOLD signal from it. I would like to know 1-if my approach is correct? 2- should I use

Re: [Freesurfer] Mri_segstats for PET data: Reviewer question

An ROI does not have a GM probabability, so I'm not sure what to say. Perhaps he/she wants the average amount of GM in the ROI relative to the size of the ROI? You can get this with mri_compute_volume_fractions. This will produce maps of the GM fraction in each voxel (separating cortical and

[Freesurfer] Mri_segstats for PET data: Reviewer question

External Email - Use Caution Hi Freesurfer Team, I have used mri_segstats to get ythe mean PET uptake across all the parcellations in the WMPARC space. These values were calculated in the native PET space (following the DTI tutorial). A reviewer asked what is the grey matter

Re: [Freesurfer] mri_segstats

From: Nasiriavanaki, Zahra Sent: Thursday, April 11, 2019 4:52:49 PM To: Freesurfer support list Subject: Re: [Freesurfer] mri_segstats Thank you so very much. Yes, the values look normal now. Mona From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of G

Re: [Freesurfer] mri_segstats

arvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Thursday, April 11, 2019 4:19:00 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] mri_segstats > The value of what is too high? > > > On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote: &g

Re: [Freesurfer] mri_segstats

vard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Thursday, April 11, 2019 4:19:00 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] mri_segstats > The value of what is too  high? > > > On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote: &g

Re: [Freesurfer] mri_segstats

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D. Sent: Thursday, April 11, 2019 4:19:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats The value of what is too high? On 4/11/19 4:07 PM, Nasiriavanaki, Zahra

Re: [Freesurfer] mri_segstats

The value of what is too  high? On 4/11/19 4:07 PM, Nasiriavanaki, Zahra wrote: > > Hi > > > I have not got the answer to my question yet, and I appreciate if you > could please let me know what you think about it. > > > Thanks > > Mona > >

Re: [Freesurfer] mri_segstats

Hi I have not got the answer to my question yet, and I appreciate if you could please let me know what you think about it. Thanks Mona From: Nasiriavanaki, Zahra Sent: Tuesday, April 9, 2019 5:55:58 PM To: Freesurfer support list Subject: mri_segstats Dear

[Freesurfer] mri_segstats

Dear Freesurferers I was trying to do a connectivity analysis using subnuclei of Amygdala. I had an Amygdala segmentation file (reg.lh.HBT.mgz for letf Amygdala) and I tried to use that in mri_segstats to extract the timeseries and then use it as a seed in my analysis. However when I looked

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

Hi Daniel left and right hippocampus have different indices (17 and 53) cheers Bruce On Wed, 6 Mar 2019, Daniel Callow wrote: External Email - Use Caution Never mind. I see that I can use those to id #'s to call from  FreeSurferColorLUT.txt. I assume that those Id's are

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

External Email - Use Caution Never mind. I see that I can use those to id #'s to call from FreeSurferColorLUT.txt. I assume that those Id's are consistent for both left and right hippocampus. Thanks for the help! *Daniel Callow* *PhD Student, Neuroscience and Cognitive Science*

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

External Email - Use Caution Hi Doug, Thank you for your reply! Unfortunately when I run the same code as before but by calling to /Applications/freesurfer/average/HippoSF/atlas/compressionLookupTable.txt instead of /Applications/freesurfer/FreeSurferColorLUT.txt and using the

Re: [Freesurfer] mri_segstats issue with hippocampal subfields

look in $FREESURFER_HOME/average/HippoSF/atlas/compressionLookupTable.txt The first number should be the one you are looking for. On 3/6/19 12:26 PM, Daniel Callow wrote: > > External Email - Use Caution > > Hello, > > I am trying to extract stats from the hippocampal subfield volumes >

[Freesurfer] mri_segstats issue with hippocampal subfields

External Email - Use Caution Hello, I am trying to extract stats from the hippocampal subfield volumes that I have warped to diffusion space. mri_vol2vol --mov /Volumes/DANIEL/dti_freesurf/dtrecon/${subj}.${cond}./lowb.nii.gz --targ

Re: [Freesurfer] mri_segstats and mris_anatomical_stats read out different # of rois

which ROIs are different? On 2/22/19 5:39 PM, Winkelbeiner, Stephanie A wrote: > > External Email - Use Caution > > Hi Freesurfers, > > I’m trying to read out GM and WM values from parcels (ROIs) but get a > different amount of ROIs for GM and WM. > > I use the following commands

[Freesurfer] mri_segstats and mris_anatomical_stats read out different # of rois

External Email - Use Caution Hi Freesurfers, I'm trying to read out GM and WM values from parcels (ROIs) but get a different amount of ROIs for GM and WM. I use the following commands (embedded in a loop), for GM mris_anatomical_stats -mgz \ -cortex

Re: [Freesurfer] mri_segstats more decimals?

There is not a way to get more decimals but you can apply a scaling factor with --mul, eg, --mul 1000 will multiply the output by 1000 On 12/19/2018 04:01 PM, Winkelbeiner, Stephanie A wrote: > > External Email - Use Caution > > Hi Freesurfer, > > Is there a way to print out more

[Freesurfer] mri_segstats more decimals?

External Email - Use Caution Hi Freesurfer, Is there a way to print out more decimals with mri_segstats? The mean diffusivity values are very small and with only four decimals not really distinguishable from each other. Thanks for your help! Stephanie The information

[Freesurfer] mri_segstats reporting more decimals

External Email - Use Caution Hi Freesurfers, Is there an option to write out more decimals when using the mri_segstats command? I'm extracting mean diffusivity values and would need at least 5 decimals to make sense of them. Thanks for your help! Cheers Stephanie The

[Freesurfer] mri_segstats - different results with --ctab

External Email - Use Caution Hi freesurfer experts, I'm trying to extract mean FA values (dti_FA.nii.gz) using a segmentation volume (parc2502dwi.nii.gz) and the corresponding color table with: for subj in SPN01*; do if [ -d "${subj}" ]; then cd $subj/ #

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

and does that file exist in /tmp? Is there space in /tmp? On 02/28/2018 01:33 PM, Yash Patel wrote: > Yes, I made sure I had permission to write into /tmp. > > On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve > > wrote: > > do

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Thanks for the advice. I did have permission to write into /tmp; however the HPC wouldn't allow it through the mri_segstats command line. The issue was resolved by making a directory in the tmp manually, and then mri_segstats works normally. Thanks, Yash On Wed, Feb 28, 2018 at 1:33 PM, Yash

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Yes, I made sure I had permission to write into /tmp. On Wed, Feb 28, 2018 at 12:23 PM, Douglas N Greve wrote: > do you have write permission to /tmp ? > > > On 02/27/2018 03:25 PM, Yash Patel wrote: > > Hello FreeSurfer experts, > > > > I am attempting to run

Re: [Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

do you have write permission to /tmp ? On 02/27/2018 03:25 PM, Yash Patel wrote: > Hello FreeSurfer experts, > > I am attempting to run "mri_segstats --annot [subjectid] lh aparc > --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" > > Whenever I try, I receive the following

[Freesurfer] mri_segstats - CTABWriteFileASCII; could not open file for writing

Hello FreeSurfer experts, I am attempting to run "mri_segstats --annot [subjectid] lh aparc --sum [outputpath] --i [inputfile] --id 1001 --id 1002 ... --id 1035" Whenever I try, I receive the following error (in error.log file);

Re: [Freesurfer] Mri_segstats on longitudinal data (NVoxels)

Also, unless something is wrong with your processing or time point naming, you should get different volumes also for each time point in the longitudinal stream. Manually open the aseg.stats and check to determine if the problem is in way you processed the longitudinal data or when creating the

Re: [Freesurfer] Mri_segstats on longitudinal data (NVoxels)

Sorry, I'm not sure what you are trying to do. Can you send command lines? On 5/9/17 6:42 AM, Ferdi van de Kamp wrote: Hi all, My question is twofold using an user specified ROI in MNI512-space I ask Freesurfer to create tables for both cross-sectionally& longitudinally processed data.

[Freesurfer] Mri_segstats on longitudinal data (NVoxels)

Hi all, My question is twofold using an user specified ROI in MNI512-space I ask Freesurfer to create tables for both cross-sectionally& longitudinally processed data. Mri_segstats performed over both cross-sectional data folders and longitudinal data folders However, when inspecting the

Re: [Freesurfer] mri_segstats

Dear Dr. Greve, Thank you for the response. I will definitely try those. Best regards, Chih-Yang Hsu On Tue, Mar 7, 2017 at 9:34 AM, Douglas Greve wrote: > There are no more moments you can get from it. You're best bet is to load > the thickness (read_curv.m) and

Re: [Freesurfer] mri_segstats

There are no more moments you can get from it. You're best bet is to load the thickness (read_curv.m) and aparc (read_annotation) maps into matlab and then do what you want with them. On 3/7/17 9:14 AM, Chih-Yang Hsu wrote: Hi, I am using Freesurfer to estimate cortical thickness. Is there

Re: [Freesurfer] mri_segstats

Dear Dr. Fischl, Thank you for the fast response. We would like to obtain the entire distribution of the cortical thickness so we can calculate more statistical, such as the first and third quartile. I tried read_cuv.m and it works perfect. Thank you again. Best regards, Chih-Yang Hsu On

Re: [Freesurfer] mri_segstats

not sure exactly what you mean, but you can use read_curv.m to load the entire spatial map of thickness into matlab for each subject. If you tell us what you want to do we can give you more detailed advice cheers Bruce On Tue, 7 Mar 2017, Chih-Yang Hsu wrote: > Hi, I am using Freesurfer to

[Freesurfer] mri_segstats

Hi, I am using Freesurfer to estimate cortical thickness. Is there any way to get all the details of the thickness distribution? I used mri_segstats but it only provided mean and standard deviation. Thank you. ___ Freesurfer mailing list

Re: [Freesurfer] mri_segstats

That is everything that has a segmentation number = 0. You can exclude it with, --excludeid 0 On 02/24/2017 10:08 AM, John Anderson wrote: > Dear Freesurfer experts, > I have used the following commandline to generate the final statistics > in my analysis: > mri_segstats --seg aseg.mgz

[Freesurfer] mri_segstats

Dear Freesurfer experts, I have used the following commandline to generate the final statistics in my analysis: mri_segstats --seg aseg.mgz --ctab-default --i suvr.nii --mask mask.nii --sum stats.dat The final output of this command is (attached). Depedning on the anatomical location of the

Re: [Freesurfer] MRI_segstats for adc.nii from dt recon - increasing decimal digits

You can add --mul 1000 to multiply everything by 1000 On 10/11/16 4:47 PM, Chung, Yoonho wrote: Hi! I ran mri_segstats as instructed in the wiki to extract ADC values from adc.nii. And as you can see below in my output, I think the decimal digits are truncated and missing the following

[Freesurfer] MRI_segstats for adc.nii from dt recon - increasing decimal digits

Hi! I ran mri_segstats as instructed in the wiki to extract ADC values from adc.nii. And as you can see below in my output, I think the decimal digits are truncated and missing the following decimal values. Is there an option or other way to get around this problem and extract ADC values from

Re: [Freesurfer] mri_segstats

mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Monday, July 18, 2016 6:56 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_segstats > > Your suvr is axially sliced whereas the anatomical is corronally slic

Re: [Freesurfer] mri_segstats

: [Freesurfer] mri_segstats Thank you Doug, Kindly how can I make the suvr and the anatomical images in the same slice? -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 18, 2016 6:56 PM

Re: [Freesurfer] mri_segstats

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats Your suvr is axially sliced whereas the anatomical is corronally sliced. They must be in exact pixel-for-pixel alignment for mri_segstats to work. On 07/18/2016 06:27 PM, Alshikho, Mohamad J. wrote: > Thank you Doug! > > Attached is

Re: [Freesurfer] mri_segstats

nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Monday, July 18, 2016 5:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_segstats > > What do you mean you got 0s only for the cblum segs? Did all other segs have > non-zeros, but clbum have 0s? And

Re: [Freesurfer] mri_segstats

: [Freesurfer] mri_segstats I'm at a loss as to why that is the case. Can you send the PET.anat.mgz and wmparc.mgz to our filedrop? On 07/18/2016 06:14 PM, Alshikho, Mohamad J. wrote: > Thank you Doug! > > Attached is a report for one of the subjects showing how the > cerebellum structure

Re: [Freesurfer] mri_segstats

Of Douglas N Greve > Sent: Monday, July 18, 2016 5:45 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mri_segstats > > What do you mean you got 0s only for the cblum segs? Did all other segs have > non-zeros, but clbum have 0s? And did you get non-0s in the 2nd commandline? &

Re: [Freesurfer] mri_segstats

urfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 18, 2016 5:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats What do you mean you got 0s only for the cblum segs? Did all other segs have non-zeros, but clbum have 0s? And did you get non-0s in the 2nd c

Re: [Freesurfer] mri_segstats

urfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Monday, July 18, 2016 5:45 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats What do you mean you got 0s only for the cblum segs? Did all other segs have non-zeros, but clbum have 0s? And did you get non-0s in the 2nd c

Re: [Freesurfer] mri_segstats

lated to a missing flags in my "mri_segstats" command line? > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve > Sent: Thursday, July 7, 2016 12:17 PM > To

Re: [Freesurfer] mri_segstats

The first one On 07/06/2016 08:22 PM, Alshikho, Mohamad J. wrote: > > Dear FS experts, > > I have PET image "pet.anat.mgz" in subject space. I want to calculate > the mean PET signal for every parcellate and segment in the atlas > "wmparc.mgz". > > _Which one of the following commands is more

[Freesurfer] mri_segstats

Dear FS experts, I have PET image "pet.anat.mgz" in subject space. I want to calculate the mean PET signal for every parcellate and segment in the atlas "wmparc.mgz". Which one of the following commands is more accurate? 1. mri_segstats --seg $SUBJECTS_DIR/${subj}/mri/wmparc.mgz --ctab

Re: [Freesurfer] mri_segstats flags

Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats This is for linux. If that is not your system, tell me what your system is doug On 04/13/2015 02:22 PM, Alshikho, Mohamad J. wrote: Hi Doug, Kindly I have the following questions regarding the command

Re: [Freesurfer] mri_segstats flags

...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 13, 2015 3:22 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats flags Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats This is for linux

[Freesurfer] mri_segstats flags

Hi Doug, Kindly I have the following questions regarding the command mri_segstats: * I wanted to use the flag --seg-erode 2 in the command mri_segstats but I am receiving an error message that this flag is not available ( I am using FreeSurfer 5.3.0 ). * When the command

Re: [Freesurfer] mri_segstats flags

To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats flags Are you sure you're using the new version? what do you get if you type which mri_segstats On 04/13/2015 03:41 PM, Alshikho, Mohamad J. wrote: Hi Doug, My system is Linux Centos 7 I tried to run it and I got

Re: [Freesurfer] mri_segstats flags

...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 13, 2015 4:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats flags Are you sure you're using the new version? what do you get if you type which mri_segstats On 04/13/2015

Re: [Freesurfer] mri_segstats flags

...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 13, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats flags maybe zeke can help you sort it out On 04/13/2015 04:24 PM, Alshikho, Mohamad J. wrote: I got

Re: [Freesurfer] mri_segstats flags

? 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: Monday, April 13, 2015 4:29 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats flags

Re: [Freesurfer] mri_segstats flags

...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, April 13, 2015 4:52 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mri_segstats flags Only the structures in the color table (--ctab) are reported; the 1st ctab

Re: [Freesurfer] mri_segstats flags

Subject: Re: [Freesurfer] mri_segstats flags Try this one ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats This is for linux. If that is not your system, tell me what your system is doug On 04/13/2015 02:22 PM, Alshikho, Mohamad J. wrote: Hi Doug, Kindly I have

Re: [Freesurfer] Mri_segstats

There is not a flag to control the printing format. However, you can multiply the values by a constant (--mul flag). Eg, you can multiply all values by 100 or divide by 100. doug On 1/30/15 11:42 AM, Alshikho, Mohamad J. wrote: Dear FS Experts, In order to generate the statistics using

[Freesurfer] Mri_segstats

Dear FS Experts, In order to generate the statistics using mri_segstats I ran the following command line: mri_segstats --seg${in}/${i}/mri/aparc+aseg.mgz --ctab-default --i ${insa}/${i}/fa.anat.nii --mask ${insa}/${i}//svs.anat.nii --sum ${insa}/${i}/fa.summary.dat In the final report

Re: [Freesurfer] mri_segstats question

It is helpful to have a command line, but I think I can figure it out from what you have written. The first row is everything outside your seg. The second is everything inside your seg. doug On 06/25/2014 05:54 PM, Martins, Brad wrote: Hi everyone, I’m new to Freesurfer and I have a

Re: [Freesurfer] mri_segstats question

Thanks Doug, That is what I needed to know! Brad On Jun 26, 2014, at 11:13 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: It is helpful to have a command line, but I think I can figure it out from what you have written. The first row is everything outside your seg. The second is

[Freesurfer] mri_segstats

Hi, I have two questions about mri_segstats. I want to measure the surface area of a functionally-defined ROI. I used the mri_segstats as below and I want to be sure that it is correct. Please note that ROIs were defined in the native space. mri_segstats --i $SUBJECTS_DIR/SBJ1/surf/rh.area

Re: [Freesurfer] mri_segstats question

Hi Doug, Thanks again for your help. I had two questions that came up from doing some preliminary analysis with the mri_segstats: 1) When running the mri_segstats command with --seg aparc+aseg_nocortex.mgz (which is the result of the matlab code you provided below) and with --seg wmparc.mgz,

Re: [Freesurfer] mri_segstats question

On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks again for your help. I had two questions that came up from doing some preliminary analysis with the mri_segstats: 1) When running the mri_segstats command with --seg aparc+aseg_nocortex.mgz (which is the result of

Re: [Freesurfer] mri_segstats question

On 04/24/2014 09:40 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks again for your help. I had two questions that came up from doing some preliminary analysis with the mri_segstats: 1) When running the mri_segstats command with --seg aparc+aseg_nocortex.mgz (which is the result of

Re: [Freesurfer] mri_segstats question

Hi Doug, Thanks again for your reply. One last question: The aseg.mgz file includes the cortex as well. If I want to extract the cortex from the aseg.mgz file, should I binarize both the aseg.mgz and aparc_aseg.mgz files and subtract them, and then use the result in the mri_segstats command, or

Re: [Freesurfer] mri_segstats question

If you want the volume of cortex, you should definitely not use aseg.mgz. aparc+aseg is better, but the best is to use the surface-based measure found in aseg.stats doug On 04/22/2014 10:55 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks again for your reply. One last question: The

Re: [Freesurfer] mri_segstats question

Hi Doug, I'm sorry, what I meant to ask in the previous question is whether there is a way to come up with a segmentation volume for the mri_segstats command that is exactly like aseg.mgz but that does not include the cortex. The reason I'm asking is because by using the aseg.mgz volume in the

Re: [Freesurfer] mri_segstats question

You can just do it in matlab, somethhing like a = MRIread('aparc+aseg.mgz'); ind = find(a.vol 999); a.vol(ind) = 0; MRIwrite(a,'nocortex.mgz') On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, I'm sorry, what I meant to ask in the previous question is whether there is a

Re: [Freesurfer] mri_segstats question

That is great, Thanks a lot, Doug! You can just do it in matlab, somethhing like a = MRIread('aparc+aseg.mgz'); ind = find(a.vol 999); a.vol(ind) = 0; MRIwrite(a,'nocortex.mgz') On 04/22/2014 11:38 AM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, I'm sorry, what I meant to ask in

Re: [Freesurfer] mri_segstats question

On 4/18/14 3:32 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi FS community, I had some questions regarding the mri_segstats command: 1) In the excludeid flag, are the ids the ones shown in the FreeSurferColorLUT.txt? Yes 2) In case I would like to measure the mean intensity of the orig file as

Re: [Freesurfer] mri_segstats question

Hi Doug, Thanks for the quick reply! In addition: 1) The average intensity measure in the above example does not include the intensity of the skull, just everything inside, right? 2) Just to be clear on the purpose of including the segmentations in the command line: The segmentations only

Re: [Freesurfer] mri_segstats question

On 4/18/14 4:25 PM, pfot...@nmr.mgh.harvard.edu wrote: Hi Doug, Thanks for the quick reply! In addition: 1) The average intensity measure in the above example does not include the intensity of the skull, just everything inside, right? It includes all the structures that are segmented in

[Freesurfer] mri_segstats - Manual Parcellation

Hello Freesurfers, I am manually parcellating a cerebellum using Freeview and would like to compare #voxels across filled-in ROIs for reliability control. When using mri_segstats, which should be my segmentation volume? I have included my parcellation volume in the --mask option to target the

Re: [Freesurfer] mri_segstats - Manual Parcellation

you have the right segmentation volume. You do not need a mask (if a mask is given, it only reports the number of voxels in the mask) On 02/04/2014 01:38 PM, Gonzalo Iribarne wrote: Hello Freesurfers, I am manually parcellating a cerebellum using Freeview and would like to compare #voxels

Re: [Freesurfer] mri_segstats url in 5.3.0 release notes does not exist

Hi Jonathan, see my email from earlier about the new permanent location for mri_segstats doug On 10/30/2013 12:26 PM, Jonathan Harlap wrote: The version of mri_segstats that fixes the issue where mri_segstats fails unless -autorecon3 is run returns a file not found at the url

Re: [Freesurfer] mri_segstats url in 5.3.0 release notes does not exist

Thanks Doug, I did see that. Cheers, Jonathan On Nov 4, 2013, at 6:23 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Hi Jonathan, see my email from earlier about the new permanent location for mri_segstats doug On 10/30/2013 12:26 PM, Jonathan Harlap wrote: The version of

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