Re: [Freesurfer] Segmentation of hippocampal subfields

en I run the command, it gives me this error: >> >> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ segmentHA_T1.sh >> sub-002_ses-BSL >> segmentHA_T1.sh: command not found >> rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop/CAN_RUTI $ >> >> >> Any idea what

Re: [Freesurfer] Segmentation of hippocampal subfields

`segmentHA_T1.sh` again. > > -Paul > > > On Wed, Jul 7, 2021 at 12:39 PM Rosalia Dacosta Aguayo < > rdacos...@gmail.com> wrote: > >> External Email - Use Caution >> >> Hi Paul, >> >> Thank you very much for answering my question. I set

Re: [Freesurfer] Segmentation of hippocampal subfields

ork that way. > > Thanks and Regards > Nayan Wadhwani > > > On Wed, Jul 7, 2021 at 10:27 PM Rosalia Dacosta Aguayo < > rdacos...@gmail.com> wrote: > >> External Email - Use Caution >> >> Hi Paul, >> >> I did it: >> >&g

Re: [Freesurfer] Segmentation of hippocampal subfields

> What version of FreeSurfer is installed at /usr/local/freesurfer? Can you > run the following command and copy the output > > cat $FREESURFER_HOME/build-stamp.txt > > -Paul > > On Wed, Jul 7, 2021 at 1:58 PM Rosalia Dacosta Aguayo > wrote: > >> Extern

Re: [Freesurfer] Segmentation of hippocampal subfields

fswiki%2FHippocampalSubfields> > > Otherwise, if you upgrade to the latest version (v7.1.1) you can use > the segmentHA_T1.sh script. > > -Paul > > On Wed, Jul 7, 2021 at 2:29 PM Rosalia Dacosta Aguayo > wrote: > >> External Email - Use Caution >&

Re: [Freesurfer] Segmentation of hippocampal subfields

recon-all -s sub-002_ses-BSL -hippocampal-subfields-T1 > > -Paul > > On Wed, Jul 7, 2021 at 3:21 PM Rosalia Dacosta Aguayo > wrote: > >> External Email - Use Caution >> >> Hi Paul, >> >> Thank you. >> >> The think is that I a

[Freesurfer] BERT - Example of segmentation

External Email - Use Caution Dear Freesurfer team, It is my first time editing wm segmentation (white matter segmentation errors + topological errors). I wonder if there is a good tutorial on which I could rely. Also, I have read there is an example of segmentation that comes wi

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution Thank you! Rosie On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton wrote: > External Email - Use Caution > > Hi Rosie, > > >> It is my first time editing wm segmentation (white matter segmentation >> errors + topological errors). >> >> I wonder

Re: [Freesurfer] BERT - Example of segmentation

External Email - Use Caution Hi Paul, Not sure what command I should run when I edit the brainmask because the pial got too much. Kind regards, Rosie On Thu, Jul 8, 2021 at 6:13 PM Paul Wighton wrote: > External Email - Use Caution > > Hi Rosie, > > >> It is my firs

[Freesurfer] Control points and white matter segmentation

External Email - Use Caution Dear Freesurfer team, Sorry for this basic question. I wonder if once I have edited the white matter (topological defects), I can run control points without deleting what I have done to white matter segmentation. Kind regards, Rosie _

Re: [Freesurfer] Control points and white matter segmentation

; Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta > Aguayo > *Sent:* Wednesday, July 21, 2021 5:10 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Control points and

Re: [Freesurfer] recon-all crash errors (fMRIPrep)

External Email - Use Caution Hi Rubina, How did you gzip your data? Which software did you use? Kind regards, Rosie On Mon, Sep 13, 2021 at 5:59 PM Rubina Chandnani < rubinachandn...@hotmail.co.uk> wrote: > External Email - Use Caution > > Hi there, > > I'm getting i

Re: [Freesurfer] recon-all crash errors (fMRIPrep)

k> wrote: > External Email - Use Caution > > Hi Rosie, > > I used MRIcroGL to convert DICOMs to Niftis. > > Kind regards, > > Rubina > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.

Re: [Freesurfer] recon-all crash errors (fMRIPrep)

n I do in this > case? > > Thank you and best regards, > > Rubina > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Rosalia Dacosta > Aguayo > *Sent:* Monday, September 13, 2021

[Freesurfer] Basic question

External Email - Use Caution Dear Freesurfer team, I know this is a basic question, but I would like to be sure before proceeding. Are those statements below right? For cortical thickness, I should covariate for age and sex For volume, I should covariate only for TBV Thank you

Re: [Freesurfer] Basic question

ut from an analysis standpoint those are the two big differences > > Bruce > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Rosalia Dacosta > Aguayo > *Sent:* Sunday, November 21, 2021 1:42 PM > *To:*

[Freesurfer] Fwd: INS Meeting

External Email - Use Caution FYI!! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] I cannot edit white matter mask

; voxels don't change). Also note that you only need to change the wm.mgz if > the surfaces are not following the gray white boundary. It is not used for > anything else. > > On 1/27/2022 8:41 AM, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > Dear Fr

[Freesurfer] Freesurfer question about recon-all

External Email - Use Caution Dear Freesurfer group, Could you tell me which is the flag I need to use to get all the brain parcellation when I run recon-all? It seems I am getting the tables with few volumes and I guess there is something wrong. Best wishes and Merry Christmas,

Re: [Freesurfer] Freesurfer question about recon-all

External Email - Use Caution Maybe is -qcache ? On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo wrote: > Dear Freesurfer group, > > Could you tell me which is the flag I need to use to get all the brain > parcellation when I run recon-all? It seems I am

Re: [Freesurfer] Freesurfer question about recon-all

10:11 AM, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > Maybe is -qcache ? > > > > > On Wed, Dec 21, 2022 at 4:10 PM Rosalia Dacosta Aguayo < > rdacos...@gmail.com> wrote: > >> Dear Freesurfer group, >> >> Could y

Re: [Freesurfer] Freesurfer question about recon-all

External Email - Use Caution I do not get the cingulate, for example... On Wed, Dec 21, 2022 at 4:35 PM Rosalia Dacosta Aguayo wrote: > Hi Douglas, > > I am only getting the main volumes like putamen right and left, amygdala, > right and left...just gross anatom

[Freesurfer] Aseg stats question

External Email - Use Caution Dear Freesurfer team, I have found a warning about not using amygdala, hippocampus and brainstem volumes from asegstats file. I wonder if that is true. Best wishes, Rosie ___ Freesurfer mailing list Freesu

Re: [Freesurfer] Aseg stats question

External Email - Use Caution Thank you for the clarification, Douglas. Kind regards, Rosie On Thu, Jan 5, 2023 at 3:21 PM Douglas N. Greve wrote: > no, it is not > > On 1/4/2023 9:20 AM, Rosalia Dacosta Aguayo wrote: > > External Email - Use

Re: [Freesurfer] Why is this happening?

gt; > On 5/4/2023 1:34 PM, Rosalia Dacosta Aguayo wrote: > > External Email - Use Caution > Dear Freesurfer's experts, > > Why is this happening? > > Kind regards, > Rosie > > > > ___ > Freesurfer

Re: [Freesurfer] Why is this happening?

different so I changed the values and then it appeared as always. Thank you for your time! Kind regards, Rosie On Thu, May 4, 2023 at 7:55 PM Rosalia Dacosta Aguayo wrote: > Why is the brain white? > > I have been changing the thresholds and nothing seems to work... > > Kind r

[Freesurfer] control.dat not working

External Email - Use Caution Dear Freesurfer subjects, After saving my control.dat file into the tmp folder and running the command line recon-all -autorecon2-cp -autorecon3 -s It does not seem to parse the control.dat file correctly and find the control points. This is what

Re: [Freesurfer] Problem with aparcstats2table

eliminate the message and any attachments it carries from your account. On Fri, Mar 28, 2025 at 7:13 PM Rosalia Dacosta Aguayo wrote: > Dear Freesurfer team, > > I am having a trouble with aparcstats2table I have never seen before and I > do not know how to solve it. > >

Re: [Freesurfer] Problem with aparcstats2table

eliminate the message and any attachments it carries from your account. El mar, 15 abr 2025, 19:22, Douglas N. Greve escribió: > First of all, can you confirm that that file exists and is readable by > you? > > On 3/28/2025 2:31 PM, Rosalia Dacosta Aguayo wrote: > > Ex

[Freesurfer] Problem with aparcstats2table

External Email - Use Caution Dear Freesurfer team, I am having a trouble with aparcstats2table I have never seen before and I do not know how to solve it. I have run it with --help and still I don't quite understand it. Any help would be appreciated. Kind regards, Rosie ros

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