[Freesurfer] To get postings

vittalkor...@gmail.com *Best* *Vittal* ___ Freesurfer mailing list Freesurfer@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 yo

[Freesurfer] Zeroes for few regions in 'aparc.a2009s' parcellation.

External Email - Use Caution Hello Freesurfer developers, I ran recon-all command to extract all subjects stats. Here I'm mainly targetting the surface area, volume, thickness and mean curve for all subjects. " recon-all -i /filepath/file/ -s /subjectid/ -all " this was the comma

[Freesurfer] qdec analysis with more than 2 covariates

External Email - Use Caution Hi Doug, Recently I started working on freesurfer for volume based analysis. For QDEC, I need to include more than 2 variables. For example if I include patients who hail from different places like statutory town, census town and rural. In present scen

Re: [Freesurfer] qdec analysis with more than 2 covariates

laceCensus LivingplaceCensus* *Input 15 BirthplaceCensus UpbringingplaceCensus LivingplaceCensus* *Input 18 BirthplaceRural UpbringingplaceCensus LivingplaceCensus* * Thank you* *Best* *Vittal* On Mon, Oct 15, 2018 at 7:45 PM vittal korann wrote: > Hi Doug, > > Recently I started working on fr

[Freesurfer] ERROR: QdecDataTable::GetFactor: '' is not in datatable!

External Email - Use Caution Hi Freesurfer people, I'm running the QDEC on schizophrenia and controls group. Some mystery error is occurring frequently. Due to this error, I'm not able to work properly. Below is the error message in italic. Continuous Factors: Mean:

[Freesurfer] FreeSurfer crashing

External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to run recon-all on schizophrenia patients and controls. For some reason freesurfer is crashing. I wanted to know the reason for frequent crashing. I'm using Ubuntu 16.04 LTS and freesurfer-Linux-centos6_x8

[Freesurfer] Different aparc values

External Email - Use Caution Hello FreeSurfer experts, I'm planning to run QDEC on Schizophrenia and controls. To do that I ran recon-all for few subjects in 2 different systems. Both systems have ubuntu 16.04 OS but different freesurfer versions. One is using FS version6 and othe

[Freesurfer] error while running pial_lgi for gyrification index

External Email - Use Caution Hi FS experts, I wanted to run the gyrification index for all patients with Schizophrenia and volunteers. When I entered the command: "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output " Subject Stamp: freesurfer-Linux-centos6_

Re: [Freesurfer] Freesurfer Digest, Vol 185, Issue 9

eming ) >4. Re: recon-all Error : inputs cannot have multiple frames. > (Bruce Fischl) >5. error while running pial_lgi for gyrification index > (vittal korann) >6. Re: error while runni

[Freesurfer] pial.lgi

External Email - Use Caution Hi FS experts, I wanted to run the gyrification index for all patients with Schizophrenia and volunteers. When I entered the command: "recon-all -s SATM124 -qcache -measure pial_lgi" and the terminal output " Subject Stamp: freesurfer-Linux-centos6_

[Freesurfer] Undefined function or variable called 'fspecial'

External Email - Use Caution Hello FS experts, I am trying to run the gyrification index and not able to move in the right direction. When execute this command "recon-all -s CSRI005 -localGI" and here is the output copied from the terminal "#@# Local Gyrification Index lh Wed Jul

[Freesurfer] Qdec error

External Email - Use Caution Dear FreeSurfer experts I ran QDEC and got the following error. Design matrix -- 1.0 1.04000 -1.38574 2.0 29.0 19.0; 1.0 1.04000 -0.55066 2.0 35.0 19.0; 1.0 1.03000 2.31721

Re: [Freesurfer] Qdec error

External Email - Use Caution Dear Douglas I did normalize ICV values. This is something else I guess. With regards Vittal On Tue, Jan 21, 2020 at 6:09 PM vittal korann wrote: > Dear FreeSurfer experts > > I ran QDEC and got the following error. > >

[Freesurfer] WM & GM mean thickness

External Email - Use Caution Dear FreeSurfer experts I'm trying to get global mean thicknesses of white matter and gray matter separately. But *stats* folder in the *subjects *list does not mention explicitly. Is there a way to get these two thicknesses? Any assistance would be a

Re: [Freesurfer] Mean Gyrification index

My confusion is that which row I should take it as a mean gyrification value for the left hemisphere (seg or seg0001)? Please guide me if there is a way to combine two hemispheric values and make it as mean gyrification alike mean thickness. With regards Korann On Wed, Sep 9, 2020 at 4:51 PM vi

[Freesurfer] mean gyrification index

External Email - Use Caution Thank you so much, Douglas. Could you please guide me to obtain the global mean gyrification index for each subject? With regards korann ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

Re: [Freesurfer] mean gyrification index

gt; You can use mri_segstats with the --slabel option, specifying the > ?h.cortex.label and using the gyrification as input > > On 9/9/2020 12:54 PM, vittal korann wrote: > > External Email - Use Caution > Thank you so much, Douglas. > > Could you please guide me to obtain the gl

Re: [Freesurfer] mean gyrification index

Douglas N. Greve wrote: > You need to include the hemisphere in the --slabel arguments (maybe the > 2nd one) > > On 9/9/2020 2:10 PM, vittal korann wrote: > > External Email - Use Caution > Dear Douglas > > Thank you for your help! > > I got an error

Re: [Freesurfer] mean gyrification index

; (you have to replace) > > On 9/9/2020 2:26 PM, vittal korann wrote: > > External Email - Use Caution > I did that, but the error remains the same. > >> mri_segstats --slabel CSRI001 ?h $SUBJECTS_DIR/CSRI001/label/?h.cortex >> --i $SUBJECTS_DIR/CSRI001/surf/?

Re: [Freesurfer] mean gyrification index

send the actual command you ran and all the terminal output? > > On 9/10/2020 12:58 AM, vittal korann wrote: > > External Email - Use Caution > Yes, I did replace question marks with left and right. > > Thank you so much, Douglas. > > With regards > Vittal

Re: [Freesurfer] mean gyrification index

, Douglas.* So far I was able to get mean gyrification values for each hemisphere separately. *What?* I want to club the left and right hemisphere values into a single value. On Thu, Sep 10, 2020 at 9:50 PM Douglas N. Greve wrote: > > > On 9/10/2020 12:08 PM, vittal kor

Re: [Freesurfer] mean gyrification index

External Email - Use Caution Thank you so much, Douglas. On Thu, Sep 10, 2020 at 10:20 PM Douglas N. Greve wrote: > Can't you just average the lh and rh values? You can weight by the surface > area or number of vertices > > On 9/10/2020 12:53 PM, vi

[Freesurfer] fwhm values for gyrification index analysis

External Email - Use Caution Hi Doug I'm analyzing the gyrification values between schizophrenia and healthy volunteers. While performing group analysis in QDEC, I encountered an error when setting the smoothing (fwhm) parameter to 25. Here is the error message from the terminal o

[Freesurfer] Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Hi FreeSurfer experts Recently I started working on the longitudinal data. I followed the pipeline described in the below link. Also, I attached my longitudinal table along with freesurfer data. https://secure-web.cisco.com/1DF2osKRIq2P6tkekGvGP9Janom

Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Dear FreeSurfer experts This is just a gentle reminder for my query! Looking forward to your assistance to resolve the issue. With regards Korann On Tue, Nov 17, 2020 at 1:16 PM vittal korann wrote: > Hi FreeSurfer experts > > Recently

Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Dear FreeSurfer experts Just a gentle reminder! Please do help me to resolve this issue. With regards Korann On Thu, Nov 19, 2020 at 11:54 AM vittal korann wrote: > Dear FreeSurfer experts > > This is just a gentle reminder for

[Freesurfer] Fwd: Error in longitudinal pipeline {Disarmed}

External Email - Use Caution Hi FreeSurfer experts Recently I started working on the longitudinal data. I followed the pipeline described in the below link. Also, I attached my longitudinal table along with freesurfer data. https://secure-web.cisco.com/10GeKQWbNwmdQQgtn3lkt2V_V6C

[Freesurfer] Fwd: Error in longitudinal pipeline {Disarmed}

External Email - Use Caution -- Forwarded message - From: vittal korann Date: Tue, Nov 17, 2020 at 1:16 PM Subject: Error in longitudinal pipeline To: Hi FreeSurfer experts Recently I started working on the longitudinal data. I followed the pipeline described

Re: [Freesurfer] Freesurfer Digest, Vol 201, Issue 34 {Disarmed}

D1pIIx5fysVGpg4RtvwrL607Pih1qLP1T4vZqNQE-D0rl9-4jHxg3_azdbkkMQ/http%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fpipermail%2Ffreesurfer%2Fattachments%2F20201123%2F7dc628cf%2Fattachment-0001.html > > ------ > > Message: 3 > Date: Mon, 23 Nov 2020 13:13:

Re: [Freesurfer] Freesurfer Digest, Vol 201, Issue 34 {Disarmed}

CM.C matrix as per my study requirements. Hoping for your guidance! With regards Vittal On Tue, Nov 24, 2020 at 10:30 PM vittal korann wrote: > Thanks, Kersten! > > The design matrix X has a dimension of 47x6 and the contrast matrix CM.C > has a dimension of 3x17. > I wish to kn

Re: [Freesurfer] Longitudinal pipeline {Disarmed}

reesurfer list, so I suggest moving > the discussion back to there. > > Best, > > Kersten > > Am 27.11.2020 um 18:21 schrieb vittal korann : > > Hi Kersten > > Thank you for kind response. > > I think we need to talk about the design matrix X first (sorry,

[Freesurfer] Fwd: Longitudinal pipeline

External Email - Use Caution Hello FS experts Thank you for your kind response. This is regarding my previous mail. I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all).

Re: [Freesurfer] Longitudinal pipeline {Disarmed}

201123%2F7dc628cf%2Fattachment-0001.html > -- > Message: 3 > Date: Mon, 23 Nov 2020 13:13:30 + > From: "Diers, Kersten /DZNE" > Subject: Re: [Freesurfer] Error in longitudinal pipeline {Disarmed} > To: Freesurfer support

[Freesurfer] need assistance to decode QDEC results

External Email - Use Caution Dear FreeSurfer experts, I was running group interaction (for diagnosis and birthplace) in QDEC with gyrification as a dependent variable and age, gender as nuisance factors. In diagnosis, we have 2 groups: i) schizophrenic patients ii) healthy volunte

Re: [Freesurfer] Error in longitudinal pipeline

External Email - Use CautionHi KerstenThank you for kind response.I think we need to talk about the design matrix X first (sorry, I did not look at your xlsx file; I think it's probably better to send simple csv files if at all).I attached longitudinal data in csv format. Besides th

Re: [Freesurfer] Error in longitudinal pipeline {Disarmed}

up. This precludes, as far as I can see, a > clear interpretation of any changes in Y that you might observe. If you > still want to go ahead and test the time/treatment effect, just set the > corresponding element of the contrast vector to +1 or -1. > > Best, > > Kersten > &g

Re: [Freesurfer] need assistance to decode QDEC results

External Email - Use Caution Dear FreeSurfer experts, A gentle reminder pertaining to my previous email! Thanks, *VK* On Wed, Dec 9, 2020 at 11:28 PM vittal korann wrote: > Dear FreeSurfer experts, > > I was running group interaction (for diagnosis and birthplace

Re: [Freesurfer] Freesurfer Digest, Vol 202, Issue 30 {Disarmed}

arvard.edu" > Message-ID: > Content-Type: text/plain; charset="utf-8" > > It depends on the order that you specified them. You will have four groups > SczUrban > SczRural > HVUrban > HVRural > > The interaction will be of the form > (SczUrban-SczRural

Re: [Freesurfer] Error in longitudinal pipeline

ck at this point in time. Would be glad if you could let me know where I am going off the path! Thanks, Vittal On Fri, Dec 11, 2020 at 10:29 PM vittal korann wrote: > Thanks, Kersten. > > I am sorry, I didn't see your response in the FS blog. > I will go through it once and let

[Freesurfer] Help: Aparcstats and asegstats not working

External Email - Use Caution Hi Freesurfer experts, I am trying to collate all morphological parameters like thickness, area, volume, etc. When I tried executing the command " asegstats2table --subjects Met001 met002 --hemi lh --meas area --tablefile Area_aseg_stats.txt ", i

Re: [Freesurfer] Help: Aparcstats and asegstats not working

External Email - Use Caution Thanks, for your quick response. I installed python2 and did set the default version to python 2.7.18 via aliasing. But I am getting the same old errors again. The same terminal responses were listed below. The subjects that are used for aseg/aparc are

Re: [Freesurfer] Help: Aparcstats and asegstats not working

External Email - Use Caution Thanks, Yujing, for your quick response. I tried your suggestion as well but the same error keeps appearing. $ asegstats2table --subjects Met001_1 Met002_1 Met003_1 Met005_1 Met006_1 Met007_1 Met008_1 Met009_1 Met012_1 Met013_1 Met015_1 Met016_1 Met01

Re: [Freesurfer] Help: Aparcstats and asegstats not working

r/bin/asegstats2table. Can you check it by doing ‘head > /usr/local/freesurfer/bin/asegstats2table’ at the prompt? > > > > Can you also try the following? > > 1. alias python=python2 (as suggested in previous email) > > 2. python asegstats2table –subjects … --tablefile … &g

[Freesurfer] Failing to execute QDEC

External Email - Use Caution Hi Freesurfer experts, I am trying to run Qdec on schizophrenia pre and post intervention scans. I created .dat and .levels files within the qdec folders and loaded the .dat file into qdec gui. It is suddenly crashing when I select my design and hit t

Re: [Freesurfer] Failing to execute QDEC

External Email - Use Caution Hi Freesurfer experts, I am looking forward to resolve this issue. Any help would be greatly appreciated! With regards, Vittal On Wed, Feb 22, 2023 at 3:13 PM vittal korann wrote: > Hi Freesurfer experts, > > I am trying to ru