[Freesurfer] (no subject)

External Email - Use Caution Hi. I need to be removed from the mailing list. Kindly help do the same. The id is sridevisundara...@gmail.com Regards Sridhevi ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Subject does not have a bstampfile

External Email - Use Caution Sorry, your e-mail is so much, I don't want to receive your emails anymore, please don't send them again. Thanks Replied Message | From | Huang, Yujing | | Date | 01/09/2024 05:10 | | To | Freesurfer support list | | Cc | | | Subject | Re

Re: [Freesurfer] Subject does not have a bstampfile

On Behalf Of Joanna KidonSent: Monday, January 8, 2024 3:33 PMTo: freesur...@nmr.mgh.harvard.eduSubject: [Freesurfer] Subject does not have a bstampfileExternal Email - Use Caution Hello FreeSurfer Developers,I'm attempting to compute Segmentation of hippocampal subfields and nuclei

Re: [Freesurfer] Subject does not have a bstampfile

To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Subject does not have a bstampfile External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to compute Segmentation of hippocampal subfields and nuclei of the amygdala (cross-sectional and longitudinal

[Freesurfer] Subject does not have a bstampfile

/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala, but I get the following error when I run the recon-all -all -s command: Subject does not have a bstampfile, copying /usr/local/freesurfer/7.3.2/build-stamp.txt Subject FS Version: freesurfer-linux

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

To: Freesurfer support list Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Ok, now we know stem2fname is the problem. I can’t reproduce the error

[Freesurfer] Convert in subject space after cw256

External Email - Use Caution Hi all, I am trying to convert freesurfer reconall output back in original subject space so I am following this guide: https://secure-web.cisco.com/1gX

[Freesurfer] (no subject)

External Email - Use Caution Hi all, I am trying to convert freesurfer reconall output back in original subject space so I am following this guide: https://secure-web.cisco.com/1hdoEYpcNfh6v9Yoq-8Iexo7oO3DXo3uI45KMmpjSSOcduyIGyNK6kNk9t

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

...@nmr.mgh.harvard.edu On Behalf Of Lawless, Dylan Sent: Wednesday, October 11, 2023 10:39 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution I ran

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

oun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: Wednesday, October 11, 2023 9:32 AM To: Freesurfer support list Cc: Maffei, Chiara, PHD ; Yendiki, Anastasia Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. Exter

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

ylan Sent: Wednesday, October 11, 2023 10:01 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Could you point me towards the correct log file? I am unable to loca

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution There should be a log for the command you ran. I’m wondering

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

...@nmr.mgh.harvard.edu On Behalf Of Lawless, Dylan Sent: Tuesday, October 10, 2023 10:29 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Sure thing, I have attached

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

on behalf of Huang, Yujing Sent: Tuesday, October 10, 2023 9:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution The error that you cut and paste here

Re: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found. External Email - Use Caution Hello, I am attempting to create a freesurfer v7.2.0 docker container that can run tracula on the freesurfer outputs

[Freesurfer] Error in trac-all prep intra-subject registration: if: Expression Syntax. brainmask not found.

External Email - Use Caution Hello, I am attempting to create a freesurfer v7.2.0 docker container that can run tracula on the freesurfer outputs, however, I am unable to get past the intra-subject registration step without receiving the following error:   --s sub-01 --mov

Re: [Freesurfer] (no subject)

External Email - Use Caution SVM is a segmentation/classification algorithm and does not give the inference that the GLM gives. Not sure what other models you are talking about On 8/21/2023 9:28 AM, 林 耀云 wrote: External Email - Use Caution Hi Freesurfer Team, I have

[Freesurfer] (no subject)

External Email - Use Caution Hi Freesurfer Team, I have a question can’t understand. Why just uses general linear model to analysis in Freesurfer? There are a lot of models such as nonlinear model, SVM and others. Please help me answer. Thank you so much. Additionally, as

Re: [Freesurfer] (no subject)

External Email - Use Caution Hello, 'timepoints' refers to the individual scan sessions that make up a longitudinal dataset for a subject. i.e. If a subject was scanned 3 times, say in 2010, 2015, and 2020, this subject would have 3 timepoints. One from each year they were

[Freesurfer] (no subject)

External Email - Use Caution Hello FreeSurfer Team, I recently messaged about running a longitudinal scan on a couple of images. The response told me to utilize "timepoints": For base processing, specify each timepoint with -tp <> (not the nii file). recon-all -base -tp -tp

Re: [Freesurfer] Extracting cortical thickness values for each subject using labels

mri_segstats with option '--slabel subject hemi full_path_to_label' - https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9ndTV9_ZapgsK_3NzhU8bMJOJY0uIz_LMPNGNff9ofQdi41lbl_z4LOot

Re: [Freesurfer] Variation in volume when recon-all is run 1416 times on the same subject

FreeSurfer team, We were interested in the reproducibility of multiple runs of recon-all and repeated recon-all 1416 times on the same subject. We then checked the left and right brain results for the volume obtained from the Aseg process. The right brain showed exactly the same volume, while the left

[Freesurfer] (no subject)

External Email - Use Caution Dear Freesurfer Team, Greetings. My name is dr. Pukovisa Prawiroharjo, Sp.S(K), PhD. I am a lecturer and researcher at the Department of Neurology Faculty of Medicine Universitas Indonesia (UI) in Indonesia. I am pleased to inform you that we have

Re: [Freesurfer] Extracting cortical thickness values for each subject using labels

a, > > Can you try mri_segstats with option '--slabel subject hemi > full_path_to_label' - > https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9ndTV9_ZapgsK_3NzhU8bMJOJY0uIz

Re: [Freesurfer] Extracting cortical thickness values for each subject using labels

External Email - Use Caution Hi Akansha, Can you try mri_segstats with option '--slabel subject hemi full_path_to_label' - https://secure-web.cisco.com/1_6KUKydZKeVMdsBFIq45SL3FnNI0J0vK1Oc1OGxgUci9ndTV9_ZapgsK_3NzhU8bMJOJY0uIz_LMPNGNff9ofQdi41lbl_z4LOot

[Freesurfer] Extracting cortical thickness values for each subject using labels

External Email - Use Caution Hi I have made custom labels to use as ROIs, I was wondering if there was any way to get thickness values at each vertex for a participant but just within the areas covered by specific label files, So from the lh.thickness.fwhm0.fsaverage.mgh

Re: [Freesurfer] Cannot find subject for recon-all

s Sent: Friday, May 12, 2023 4:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] Cannot find subject for recon-all External Email - Use Caution Thank you very much! It seemed to work but now it gives me another error message Pedros-Air:test1 pedrobarradas$ recon-all -i $SUBJEC

Re: [Freesurfer] Cannot find subject for recon-all

External Email - Use Caution Thank you very much! It seemed to work but now it gives me another error message Pedros-Air:test1 pedrobarradas$ recon-all -i $SUBJECTS_DIR/test1/01.nii -s $SUBJECTS_DIR/test1 -all ERROR: You are trying to re-run an existing subject with (possibly

Re: [Freesurfer] Cannot find subject for recon-all

barradas Sent: Monday, May 1, 2023 12:06 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Cannot find subject for recon-all External Email - Use Caution Hello! I have recently installed freesurfer and was attempting to reconstruc some exams but I keep getting this error

[Freesurfer] Cannot find subject for recon-all

External Email - Use Caution Hello! I have recently installed freesurfer and was attempting to reconstruc some exams but I keep getting this error message Pedros-Air:subjects pedrobarradas$ recon-all -i 01.nii. -s test1 -all ERROR: cannot find 01.nii. recon-all -s exited

[Freesurfer] Longitudinal TRACULA subject folder confusion

External Email - Use Caution Hello FreeSurfer devs, I am attempting to run a Longitudinal TRACULA analysis on 3 timepoints per subject using an HCP server. I have used the example dmrirc page (https://secure-web.cisco.com/1JykEBcpM6vAD_4qy69NGW33wNc83B

Re: [Freesurfer] moving results from fsaverage space to subject space

could we move the results from the surface space (FS average) to the original subject volumetric space? Do you need to go to fsaverage space? If all you want to do is the surface-based smoothing, then you can do it in the native space, then use mri_surf2vol to map it back into the volume. Run

Re: [Freesurfer] moving results from fsaverage space to subject space

am having difficulties figuring out how to move PET images from the fsaverage space back to the subject space. Using the PETSurfer wiki instructions for surface-based analysis, we have sampled each subject’s surface onto the surface of fsaverage using mri_vol2surf, which was then smoothed using

[Freesurfer] moving results from fsaverage space to subject space

External Email - Use Caution Hello— I am having difficulties figuring out how to move PET images from the fsaverage space back to the subject space. Using the PETSurfer wiki instructions for surface-based analysis, we have sampled each subject’s surface onto the surface

[Freesurfer] (no subject)

External Email - Use Caution Please unsubscribe me ___ 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

[Freesurfer] (no subject)

External Email - Use Caution Hello, Is it feasible to get the password to access the FreeSurfer VirtualBox VM's FS 7 2 0 Ubuntu 18 04 06.ova.7z image? I sincerely appreciate it. ___ Freesurfer mailing list

[Freesurfer] (no subject)

External Email - Use Caution Hi, I want to obtain the gyral height and the sulcal depth for every region of the aparc atlas. I know that in the file lh.sulc the positive values are the depth of the sulcus and the negative one are the height of the gyrus. How can I obtain

[Freesurfer] (no subject)

External Email - Use Caution behcetayyild...@gmail.com -- *Behçet Ayyıldız..* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is

[Freesurfer] (no subject)

External Email - Use Caution Sorry if this is a repeat email from last night, but signal 9 can mean you ran out of memory. You should try allocating more memory to the VM.. You could also try running the latest freesufer version = 7.3.2 which is compiled for Ubuntu 20 and you

[Freesurfer] (no subject)

External Email - Use Caution Hi, The FreeSurfer VM image needs a pass code to unarchive. Would you please send me the pass code? Alex ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

[Freesurfer] (no subject)

External Email - Use Caution Hi, I try to do something like that, Would anyone help me -- *GUELIB Bouchra: *Ph.D. student *Lire *Laboratory University: Constantine 2-Abdelhamid Mehri- *Algeria * Alternative email: guelibbouc...@gmail.com

Re: [Freesurfer] I cannot start my first subject.

14, 2022 7:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] I cannot start my first subject. External Email - Use Caution Good morning I installed Oracle VM virtual box i am able to work on the tutorial patient bert but when I copied dicom file of a patient I could not work

Re: [Freesurfer] (no subject)

Not sure. I think those distortions are the surface folding back in on itself, so you may need more cuts. On 5/25/2022 9:26 AM, Alberto Pisoni wrote: External Email - Use Caution Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials.

[Freesurfer] (no subject)

External Email - Use Caution Hi all, I am trying to flatten a whole hemisphere, and i created the cut patch following the tutorials. see the result here.

Re: [Freesurfer] Average subject and head size

External Email - Use Caution Thank you for the answer. So the averaged MRI has the size of the mni305. Is there a way to give it its true size? This can be problematic for children's MRIs. > Le 2 mai 2022 à 21:33, Douglas N. Greve a écrit : > > It will remain in talairach space

Re: [Freesurfer] Average subject and head size

It will remain in talairach space ( actually mni305) On 5/2/2022 1:08 PM, Sébastien Daligault wrote: > External Email - Use Caution > > Hi support, > I have a naive question about the make_average_subject function. > I want to average MRIs to create a template. > This process uses the

[Freesurfer] Average subject and head size

External Email - Use Caution Hi support, I have a naive question about the make_average_subject function. I want to average MRIs to create a template. This process uses the talairach transformation to average in a common space. Once averaged, is the MRI still in this space or is

Re: [Freesurfer] (no subject)

Just give freeview the path to whatever volume or surface you want to visualize Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Jabeur Mouna Sent: Wednesday, April 27, 2022 5:45 AM To: Freesurfer support list Subject: [Freesurfer] (no subject) External Email

[Freesurfer] (no subject)

External Email - Use Caution Hello, How can i import an image.nii from a folder different from /usr/local/freesurfer/7.2.0/subjects to visualise it with freeview ? Please! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Subject ID error with bbregister

Try just adding a line at the end of the lta file like subject 126346 On 2/22/2022 9:45 AM, Tisdall, Dylan wrote: > External Email - Use Caution > > Hi Doug and Matt, > > I'm pretty confident my $SUBJECTS_DIR is correct, its the same one I used for > recon-a

Re: [Freesurfer] Subject ID error with bbregister

External Email - Use Caution Hi Doug and Matt, I'm pretty confident my $SUBJECTS_DIR is correct, its the same one I used for recon-all on this subject and the files seem to be in the right place; wee below: [mtisdall@ftdc-gpu01 126346]$ echo $SUBJECTS_DIR /home/mtisdall

Re: [Freesurfer] Subject ID error with bbregister

Is there a blank subject line in the lta file? If so, it is probably trying to get the subject from there. You can try putting the --s after the --lta On 2/21/2022 3:43 PM, Tisdall, Dylan wrote: > External Email - Use Caution > > Hi all, > > Quick question on a

Re: [Freesurfer] Subject ID error with bbregister

ehalf of Tisdall, Dylan" wrote: Hi all, Quick question on a puzzling error with bbregister version 7.1.1. When I run: bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 I get the error: ERROR: must spec a

[Freesurfer] Subject ID error with bbregister

External Email - Use Caution Hi all, Quick question on a puzzling error with bbregister version 7.1.1. When I run: bbregister --s 126346 --mov mgz/7T_MEMPRAGE --init-reg 7Tto3Tinit.lta --reg 7Tto3T.lta --o 7TMEMPRAGE_warped.mgz --t1 I get the error: ERROR: must spec a subject

Re: [Freesurfer] Difficulty Running Single Subject Surfaced Based GLM

isXAPLRyzOFnS-FUhNnf6WkJ4aDshlD1YgdAFvaSof0Q7EdzgPMmTsek__sdyr7qIcKRNn3Vl3g6ARaRHDXMvSsFsesmqvIgyBJKDX-8AWaifiQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV5.1%2FFsFastFirstLevel> to do a surface based GLM in an individual subject (using my own data, not the tutorial data), but I am getting the following error: Error usi

[Freesurfer] Difficulty Running Single Subject Surfaced Based GLM

%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsFastTutorialV5.1%2FFsFastFirstLevel to do a surface based GLM in an individual subject (using my own data, not the tutorial data), but I am getting the following error: Error using MRIread (line 76) ERROR: cannot determine format of /subnum/bold/runnum/masks

Re: [Freesurfer] LGI - trouble creating output file for each subject

External Email - Use Caution Dear Dr. Douglas, Thank you so much for your response. I just checked in the surf folder of this specific subject and yes, rh.white does exist. Not 100% sure how to check if it's readable for freesurfer - could you please explain? Thank you! On Tue

Re: [Freesurfer] LGI - trouble creating output file for each subject

Caution Hello again FreeSurfer experts, I am having some issues creating the output file with the LGI data for each subject. Could you please help me with this? See below the code (in bold) that I used and the outputs that I got. Please let me know if you need additional information

[Freesurfer] LGI - trouble creating output file for each subject

External Email - Use Caution Hello again FreeSurfer experts, I am having some issues creating the output file with the LGI data for each subject. Could you please help me with this? See below the code (in bold) that I used and the outputs that I got. Please let me know if you

[Freesurfer] Subject with extremely large ventricles

External Email - Use Caution Hi Freesurfer Experts, Is there anything that could be done to improve the surface definitions for this particular subject (attached)? The pial and white matter boundaries  in the cortex are generally accurate though. Thank you. Best Wishes

Re: [Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

11002_MR1.long.111002 -localGI > > > > > > Here, `111002_MR1.long.111002` is assumed to be the dir with the > > > longitudinal outputs. > > > > > > Alternatively, you could try running `mris_compute_lgi` directly on the > > > pial surfaces

Re: [Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

e, `111002_MR1.long.111002` is assumed to be the dir with the > > longitudinal outputs. > > > > Alternatively, you could try running `mris_compute_lgi` directly on the > > pial surfaces of interest. > > > > -Paul > > > > On Thu, Jul 22,

Re: [Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

gitudinal outputs. > > Alternatively, you could try running `mris_compute_lgi` directly on the > pial surfaces of interest. > > -Paul > > On Thu, Jul 22, 2021 at 3:55 AM Tim Schäfer wrote: > > > External Email - Use Caution > > > > I should maybe

Re: [Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

: > External Email - Use Caution > > I should maybe add some more info to the last email: > > * The error is not subject-specific. I tried for all my subjects, and the > error is identical for all of them. > * I am aware of the face that one needs Matlab to run lGI, an

Re: [Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

External Email - Use Caution I should maybe add some more info to the last email: * The error is not subject-specific. I tried for all my subjects, and the error is identical for all of them. * I am aware of the face that one needs Matlab to run lGI, and it is on the PATH

[Freesurfer] Running local lGI for longitudinal subject gives error: Unmatchted "'"

External Email - Use Caution Dear FreeSurfer experts, I am trying to compute local lGI in FreeSurfer 6 for a subject that has undergone longitudinal processing. In this example, the longitudinal base subject folder (with the long template recon-all output for that subject

Re: [Freesurfer] (no subject)

External Email - Use Caution Hello, Can you please clarify the following: Do we use subcortical QC rating for all subcortical measures such as accumbens as well measures such as total white matter volume. We do not use it for estimated total intracranial volume as this is

Re: [Freesurfer] (no subject)

No, it should not On 6/22/2021 4:12 PM, miracle ozzoude wrote: External Email - Use Caution Hello All, I was wondering if the  Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats

[Freesurfer] (no subject)

External Email - Use Caution Hello All, I was wondering if the Right/Left-Cerebral-White-Matter in the aparc+aseg.mgz contains WM hypointensities. mri_segstats --seg aparc+aseg.mgz -i dti_fa.nii.gz --sum dti_fa.stats --ctab FreeSurferColorLUT.txt Best, Paul

Re: [Freesurfer] Problem to run recon-all in one subject

No worries, it happens to all of us  Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rosalia Dacosta Aguayo Sent: Monday, June 21, 2021 11:07 AM To: Freesurfer support list Subject: Re: [Freesurfer] Problem to run recon-all in one subject External Email - Use Caution

Re: [Freesurfer] Problem to run recon-all in one subject

Hi Rosalia Does /home/rosalia/Desktop/ARTICO/sub-001_ses-BSL_T1w exist? Shouldn’t it have an extension like .nii.gz or .mgz? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rosalia Dacosta Aguayo Sent: Monday, June 21, 2021 10:49 AM To: Freesurfer support list Subject

Re: [Freesurfer] Problem to run recon-all in one subject

Monday, June 21, 2021 10:49 AM > *To:* Freesurfer support list > *Subject:* [Freesurfer] Problem to run recon-all in one subject > > > > *External Email - Use Caution* > > Dear Freesurfer's experts > > > > I am trying to run recon-all -all in a

[Freesurfer] Problem to run recon-all in one subject

External Email - Use Caution Dear Freesurfer's experts I am trying to run recon-all -all in a subject and it seems there is a problem I do not know how to solve. rosalia@rosalia-Lenovo-Y520-15IKBN ~/Desktop $ recon-all -s sub-001_ses-BSL -i /home/rosalia/Desktop/ARTICO/sub

Re: [Freesurfer] (no subject)

External Email - Use Caution Hi Doug, I ran mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir aseg.glmdir this created a folder aseg.glmdir which contains another folder groupdiff, where sig.ghm is, I then tried to visualise results

Re: [Freesurfer] (no subject)

How did you create the sig.mgh that you are trying to overlay? On 5/28/2021 11:16 AM, Francisca Ferreira wrote: External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I  ran mri_glmfit using the

[Freesurfer] (no subject)

External Email - Use Caution Dear Experts, I have extracted subcortical vols corrected for intracranial vols using asegstats2table and I ran mri_glmfit using the following command mri_glmfit \--table aseg.txt \--fsgd newCH_deblank3.fsgd dods \--C groupdiff.mtx \--glmdir

[Freesurfer] (no subject)

External Email - Use Caution Hello, I am running into errors when running segmentHA_T2.sh ${subj} /data/bswift-1/dcallow/aging/freesurfer/${subj}/mri/T2.norm.mgz T2 1 Approximately 10% of my subjects are being processed but for some reason, the majority fail to execute. Here is

Re: [Freesurfer] Cluster correction at subject level using -log10(p) values

running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using mri_mcsim followed by mri_surfcluster and I would like to constrain my

[Freesurfer] Cluster correction at subject level using -log10(p) values

External Email - Use Caution Dear Experts, I am running an analysis where I have -log10(p) values on the cortical surface of some subjects stored as a MGH file. I would now like to run a cluster level correction on these data at the level of each individual subject using

Re: [Freesurfer] Regarding xhemi comparison of hemispheres of the same subject

, I'm currently working on comparing left with right hemisphere activation for individual subjects and using version 7.1.1. Since it is on an individual level, we would like to register the left hemisphere of each subject to their mirrored right hemisphere (or vice versa). When looking

[Freesurfer] Regarding xhemi comparison of hemispheres of the same subject

External Email - Use Caution Dear all, I'm currently working on comparing left with right hemisphere activation for individual subjects and using version 7.1.1. Since it is on an individual level, we would like to register the left hemisphere of each subject to their mirrored

Re: [Freesurfer] Difference between vox2ras and vox2ras-tkr for subject-specific T1w through FreeSurfer

On 3/21/2021 3:33 PM, Adam Li wrote: External Email - Use Caution Hi, I am a bit noob on FreeSurfer and coordinate systems and I had a few questions. I am wondering if I have the |T1.mgz| file of FreeSurfer after running recon-all and this is the 256^3 image re-scaled and

[Freesurfer] Difference between vox2ras and vox2ras-tkr for subject-specific T1w through FreeSurfer

External Email - Use Caution Hi, I am a bit noob on FreeSurfer and coordinate systems and I had a few questions. I am wondering if I have the T1.mgz file of FreeSurfer after running recon-all and this is the 256^3 image re-scaled and re-oriented from your orig.mgz file, then how

Re: [Freesurfer] must specify a subject id

External Email - Use Caution Hi liangfeng kuang, I think FreeSurfer is failing to find your subject as you set the $SUBJECTS_DIR to .../kuang_dev_results but your actual subject is in .../kaung_dev_data/... . Best, Horsng > On Feb 26, 2021, at 10:41 PM, Douglas N. Greve wr

Re: [Freesurfer] must specify a subject id

-ubuntu18_x86_64-dev/freesurfer/kuang_dev/kuang_dev_data/ch2/ch2.nii-all –qcache -parallel , then and appeared 'ERROR: must specify a subject id', what should i do to solve it? best wishes liangfeng kuang ___ Freesurfer mailing list Freesurfer

[Freesurfer] (no subject)

External Email - Use Caution Hi, Hope all are safe and well. Can anyone help me in finding any biomarker for Alzheimer's Disease or any guidance related to that? Waiting for response. Regards: Rahul Sharma Research Scholar 9827834360 *"Manners Maketh Man"*

[Freesurfer] the T2.mgz in subject/mri should be skull stripped or not?

External Email - Use Caution Hi all, I encountered a problem about the T2.mgz in subject/mri. I ran my data using recon-all -all -i T1path -s name -T2 T2path -T2pial(7.1.1 or 7.1.0), but the results were inconsistent, sometimes the mri/T2.mgz had skull sometimes it didn't

Re: [Freesurfer] Talairach Failure in recon-subject {Disarmed}

, Freesurfer team I have met a Talairach Failure problem when running the recon -all for a subject, here is the feedback: I tried -notal-check flag, but it might cause another problem when I use segmentHA_T2.sh to do hippocampus subfield segmentation. So, Could you help me to solve this problem? Thanks

[Freesurfer] Talairach Failure in recon-subject {Disarmed}

External Email - Use Caution Hi, Freesurfer team I have met a Talairach Failure problem when running the recon -all for a subject, here is the feedback: I tried -notal-check flag, but it might cause another problem when I use segmentHA_T2.sh to do hippocampus subfield

[Freesurfer] (no subject)

Dear Sir or Madam, I am not longer working with FreeSurfer so I would like to remove my subscription to the mailing list. Thank you, Laura smime.p7s Description: S/MIME cryptographic signature External Email - Use Caution___ Freesurfer

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

FREESURFER_HOME in your matlab path On 12/2/2020 8:11 PM, 李梦君 wrote: External Email - Use Caution I extracted the value of the ROI average in each subject in the standard space and imported into the SPSS 26.0 to compute the significance of the difference. -原始邮件- 发件人:"

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

External Email - Use Caution I extracted the value of the ROI average in each subject in the standard space and imported into the SPSS 26.0 to compute the significance of the difference. -原始邮件- 发件人:"Greve, Douglas N.,Ph.D." 发送时间:2020-12-02 23:31:26

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

ard.edu> 发送时间:2020-11-30 01:22:22 (星期一) 收件人: "freesurfer@nmr.mgh.harvard.edu"<mailto:freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> 抄送: 主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Dis

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

ume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} You mean that you are getting a different result between the voxel wise analysis and the ROI-wise analysis? And you created the ROI from the region that is significant in the voxel-

Re: [Freesurfer] (no subject)

No, you'll have to add it as a covariate. Or you can add --etiv when you run mris_preproc and it will divide the maps by the eTIV On 11/25/2020 3:23 PM, Sara Lyn wrote: External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

? -原始邮件- 发件人:"Douglas N. Greve" <mailto:dgr...@mgh.harvard.edu> 发送时间:2020-11-16 23:48:37 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 抄送: 主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed

[Freesurfer] (no subject)

External Email - Use Caution Hi Freesurfer experts, I'm doing a surface based volume analysis and wanted to know if there was a flag to regress out eTIV in the model. Thank you ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

control. Did this correct? -原始邮件- 发件人:"Douglas N. Greve" 发送时间:2020-11-16 23:48:37 (星期一) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

The lh_areapial.avgwf.dat has a value for each subject. That value will be whatever the y.mgh is. If you want a different value, then create a new y.mgh file. Also, I forgot to tell you to include --sumwf so that the avgwf file has the sum and not the average. On 11/14/2020 5:24 AM, 李梦君 wrote

Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

las N. Greve" 发送时间:2020-11-13 23:03:50 (星期五) 收件人: freesurfer@nmr.mgh.harvard.edu 抄送: 主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} sorry, I don't know what you are asking On 11/12/2020 8:

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