Re: [Freesurfer] Hippocampal segmentation Matlab crash

the paths to your freesurfer installation and your input/output data. Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Caitlin R Bowman Date: Wednesday, March 9, 2022 at 12:57 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash

Re: [Freesurfer] Hippocampal segmentation Matlab crash

at 3:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal segmentation Matlab crash Hi Cait, Before running the command, can you try unsetting the LD_LIBRARY_PATH variable? You can do this in bash with: unset LD_LIBRARY_PATH or in cshell with: unsetenv LD_LIBRARY_PATH be

Re: [Freesurfer] Hippocampal segmentation Matlab crash

, March 8, 2022 at 3:14 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal segmentation Matlab crash External Email - Use Caution Hello, I am trying to run the hippocampal segmentation used in freesurfer 7. I have tried with both 7.1.1 and 7.2 and have run

[Freesurfer] Hippocampal segmentation Matlab crash

External Email - Use Caution Hello, I am trying to run the hippocampal segmentation used in freesurfer 7. I have tried with both 7.1.1 and 7.2 and have run into an issue at the same spot. I am running on a computing cluster, not locally. The same code works fine on my local

Re: [Freesurfer] hippocampal segmentation differences pediatric sample

I would not expect the different subjects to be the same (they are different subjects). I don't know how you'd get them back to native space. The opposite of how you normalized them I guess. On 2/12/2022 8:15 AM, Aleksandra Lecei wrote: External Email - Use Caution Hi, I'm new to 

[Freesurfer] hippocampal segmentation differences pediatric sample

External Email - Use Caution Hi, I'm new to this and was wondering if someone could help me out? I used a T1 preprocessed image (fmriprep), normalized to the NIH pediatric cohort 6 (13-18.5 years) template to do recon-all and then used the hippocampal segmentation tool v.7. I

Re: [Freesurfer] Hippocampal segmentation - data processed in different fs version

Yes! As long as you explain it clearly in whatever paper you may write with the results ;-) Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Jan 10, 2022, at 23:28, Katarina Vulić mailto:vulic.katari...@gmail.com>> wrote:

[Freesurfer] Hippocampal segmentation - data processed in different fs version

External Email - Use Caution Hello Freesurfer Developers, We have data that has been initially processed by Freesurfer v6.0.1. Is it ok if we run hippocampal subfield segmentation (

Re: [Freesurfer] Hippocampal segmentation

It segments the whole hippocampus (ie, assigns voxels as either hippo or something else), then counts up the voxels to get the voume (also applies partial volume correction). It does not compute curvature of hippo. Hippo does form part of the boundary of the surface, but we exclude it from

Re: [Freesurfer] Hippocampal segmentation

External Email - Use Caution Then How FreeSurfer calculates the volume, curvature etc from Hippocampus and How could I check it? El vie, 26 feb 2021 a las 14:44, Douglas N. Greve () escribió: > Hippocampus is not part of the surface > > On 2/24/2021 10:40 AM, Alberto Del Cerro

Re: [Freesurfer] Hippocampal segmentation

Hippocampus is not part of the surface On 2/24/2021 10:40 AM, Alberto Del Cerro Leon wrote: External Email - Use Caution Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf and editing the labels manually. However when I was editing the labels in tksurfer the

[Freesurfer] Hippocampal segmentation

External Email - Use Caution Hello Freesurfers, I am doing an AAL atlas on freesurfer using mri_vol2surf and editing the labels manually. However when I was editing the labels in tksurfer the hippocampal field is quite bad. I tried to look the segmentation used by you in labels

[Freesurfer] HIppocampal segmentation failure with FS 7.1.1

External Email - Use Caution Dear experts, I'm currently using FS 7.1.1 and have already done hippocampal segmentation with segmentHA_T2.sh command for over 100 subjects. Most results are excellent but some segmentations are inaccurate, for example, including neighbouring white

Re: [Freesurfer] hippocampal segmentation freesurfer 7.1.0

vard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darwin-macOS-7.1.0.tar.gz > instead. > > Best > Andrew > > From: on behalf of Angela > Favaro > Reply-To: FS Help > Date: Sunday, May 24, 2020 at 3:58 AM > To: FS Help > Subject: [Freesurfer] hippocampal segmentation f

Re: [Freesurfer] hippocampal segmentation freesurfer 7.1.0

://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.1.0/freesurfer-darwin-macOS-7.1.0.tar.gz instead. Best Andrew From: on behalf of Angela Favaro Reply-To: FS Help Date: Sunday, May 24, 2020 at 3:58 AM To: FS Help Subject: [Freesurfer] hippocampal segmentation freesurfer 7.1.0 External Email - Use

[Freesurfer] hippocampal segmentation freesurfer 7.1.0

External Email - Use Caution Hi all, I realized that in the MacOS version of freesurfer 7.1.0 there is a file (for hippocampal segmentation) that is lacking. How can I obtain it? The file is a Matlab script: segmentSubjectT1_autoEstimateAlveusML.app That should be in

[Freesurfer] Freesurfer hippocampal segmentation in patient with temporal lesion

External Email - Use Caution Dear all, I have a subject for whom I need to segment the right hippocampal and amygdalar subfields. However, they have a significant white matter lesion and large ventricles in the right temporal lobe, such that skull-stripping consistently cuts

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Pradeep Reply-To: Freesurfer support list Date: Monday, 8 October 2018 at 18:51 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

(CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Pradeep < > tprad...@gmail.com> > *Reply-To: *Freesurfer support list > *Date: *Thursday, 4 October 2018 at 19:21 &g

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Pradeep Reply-To: Freesurfer support list Date: Thursday, 4 October 2018 at 19:21 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal segmentation with an additional

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

glesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of Pradeep < > tprad...@gmail.com> > *Reply-To: *Freesurfer support list > *Date: *Thursday, 4 October 2018 at 19:12 > *To: *Freesurfer support list > *Subject: *[Freesurf

Re: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

://cmictig.cs.ucl.ac.uk/ From: on behalf of Pradeep Reply-To: Freesurfer support list Date: Thursday, 4 October 2018 at 19:12 To: Freesurfer support list Subject: [Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab External Email - Use Caution Hello, I am trying

[Freesurfer] Hippocampal segmentation with an additional scan ERROR kvlGEMSMatlab

External Email - Use Caution Hello, I am trying to run the hippocampal segmentation with an additional Hi-res scan using the following command recon-all -s -hippocampal-subfields-T2 and got the following error Error using kvlGEMSMatlab

[Freesurfer] hippocampal segmentation development version question

Hi, I am interested in using the head/body/tail output from the hippocampal subfield segmentation module. Is there a reference or description of what landmarks were used to separate head/body and body/tail? Thanks! Maureen ___ Freesurfer mailing list

Re: [Freesurfer] Hippocampal segmentation flips on the left side

Hi Lauri, This error is occurring because the libstdc++.so.6 library included with the linked matlab is older than the version shipped with centos7. While I think about the best way to resolve this, setting the following environment variable before running recon-all should clear everything up

Re: [Freesurfer] Hippocampal segmentation flips on the left side

I think this is related to a matlab incompatibility. Can I see a copy of the log? Andrew > On Jan 11, 2018, at 12:09 PM, Iglesias Gonzalez, Eugenio > wrote: > > Dear Lauri, > Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so > the left model

Re: [Freesurfer] Hippocampal segmentation flips on the left side

Dear Lauri, Your problem is that GLIBCXX_3.4.15 was not found by kvlApplyTransform, so the left model was not successfully flipped to create the right model – which is why your right hippocampus appears flipped. Andrew: any ideas on how to fix this? Cheers, /Eugenio PS: the dev version does not

Re: [Freesurfer] Hippocampal segmentation flips on the left side

Dear Lauri, Would you mind sending me the log of the subfield segmentation? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 08/01/2018, 22:04,

[Freesurfer] Hippocampal segmentation flips on the left side

Dear Freesurfers, When I run freesurfer 6.0 recon-all -hippocampal-subfields-T1 command to segment an MNI152 template, the resulting segmentation of left hippocampus got flipped in left-right dimension. Otherwise the right hippocampus and other subcortical segmentations in the aseg-file look

Re: [Freesurfer] Hippocampal segmentation flips on the left side

Very weird! Can you please send us the log files? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 21/12/2017, 17:51, "freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] Hippocampal Segmentation

algary.ca> Sent: Sunday, February 26, 2017 7:54:28 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Segmentation Hi Eugenio, Thanks for getting back to me and yes it is version 5.1-5.3. I will speak to my IT department about upgrading to version 6.0, but can you let m

Re: [Freesurfer] Hippocampal Segmentation

Hi Eugenio, Thanks for getting back to me and yes it is version 5.1-5.3. I will speak to my IT department about upgrading to version 6.0, but can you let me know about the processing details for the older version in the meantime? We have already processed a group of subjects and my

Re: [Freesurfer] Hippocampal Segmentation

Hi Jessica, I believe that those are the old labels. What version of FreeSurfer are you using? 5.1 - 5.3? If so, you should upgrade to 6.0. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com

[Freesurfer] Hippocampal Segmentation

Hello FreeSurfer Team , I was wondering if you could explain to me what the “Left-Hippocampus” and “Right-Hippocampus” labels in the subfield segmentation are? Are they the tail of the hippocampi? Or everything that is not assigned to one of the other seven labels? Additionally I am wondering

[Freesurfer] Hippocampal segmentation

Hello Freesurfer Developers, I'm willing to use the new released version from Freesurfer (6.7.0) to measure the hippocampal volumes. Is that able to provide me the volumes of the anterior (hippocampal head) and posterior (hippocampal tail) parts of the Hippocampus and segmented these parts

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: Z K zkauf...@nmr.mgh.harvard.edu, freesurfer@nmr.mgh.harvard.edu Cc: e iglesias e.igles...@bcbl.eu Sent: Thursday, August 20, 2015 2:29:16 PM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files? Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

- Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta -missing files? Hello, I have installed FreeSurfer v6

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Alexandra De Araujo deara...@uoregon.edu To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, August 20, 2015 1:45:02 AM Subject: Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta

Re: [Freesurfer] Hippocampal segmentation with FreeSurfer v6 Beta - missing files?

Hello, I have installed FreeSurfer v6 (freesurfer-Darwin-mavericks-dev.tar.gz) in order to try the new hippocampal segmentation modules. I have installed it in my folder Application. Now, when I tried to run a hippocampal segmentation, I get the following error:

Re: [Freesurfer] hippocampal segmentation converting mgz to nii

Hi Lorenzo, The correct way to calculate the expected (not an integer value) number of voxels belonging to a subfield is by summing ( intensity / 255 ) across all voxels. Not sure where things go wrong: the integer values you report are a bit suspicious, or perhaps some rescaling of image

[Freesurfer] hippocampal segmentation converting mgz to nii

Dear freesurfer users, I have used freesurfer to segment hippocampal subfields. Then I used freeview to convert the derived .mgz files in .nii files for further analysis. I estimated the hippocampal subfields volumes with the command: kvlQuantifyPosteriorProbabilityImages $ FREESURFER_HOME/

Re: [Freesurfer] hippocampal segmentation

Hi Hugh, no attachments came through. Do you mean the segmentation of the hippocampus in the aseg? What version are you running? cheers Bruce On Wed, 10 Oct 2012, Hugh Pemberton wrote: Dear freesurfer crew, I'm having a few issues with segmentation around the hippocampus, I have included a

[Freesurfer] hippocampal segmentation

Dear freesurfer crew, I'm having a few issues with segmentation around the hippocampus, I have included a few screenshots of main and aux vol where the hippocampus has been excluded even with the addition of control points. Have you got any tips for rectifying this? It's happened a fair few times

Re: [Freesurfer] Hippocampal segmentation doubts

Thank you so much for your answer Koen,I understand, but now I'm having some trouble when running the command on one subject, hope you can help me.I have tried to perform the hippocampal subfields segmentation by running:recon-all -s MySubject -hippo-subfields and

Re: [Freesurfer] Hippocampal segmentation doubts

Hi Gabriel, 1. Using pre-processed data obtained with an older version of FreeSurfer should be OK, as long as you remember that the obtained results might/will be different from the ones you'd get if you had run the whole analysis from scratch. 2. The generic label hippocampus is used to denote

[Freesurfer] Hippocampal segmentation: version needed

Dear Freesurfer experts, I used freesurfer v4.3.0 on anatomical data (T1). I am trying to segment hippocampal subfields with the following command:  recon-all -s subjname -hippo-subfields unfortunately I get the following error: ERROR: Flag -hippo-subfields unrecognized I have already the files

Re: [Freesurfer] Hippocampal segmentation: version needed

Hi Lorenzo, The hippocampal subfield segmentation routines are only available from FreeSurfer 5.1, so you'll need that version to run the code. If all your data is already pre-processed with an older version of FreeSurfer, you might be able to simply run the hippocampal subfield segmentation

[Freesurfer] Hippocampal segmentation doubts

Dear Freesurfer expertsI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've

[Freesurfer] Hippocampal segmentation

Dear FreesurfersI'm starting to deal with the FS v5.1 hippocampal subfields segmentation, and I have a couple doubts...If I have my subjects segmented from an older FS version, Would be any problem when running the -hippo-subfields?I'm guessing not, but I wanna be sure. Because, as I've looked the

[Freesurfer] hippocampal segmentation

Hello, I converted the aseg. mgz files to nii format and created a hippcampal mask with 3dcalc. Using AFNI I opened the hippocampal mask as overlay on the brainmask .nii image as underlay. For some subjects the hippocampus is not at the correct position. Please advise. Thanks, Rashmi.

Re: [Freesurfer] hippocampal segmentation

Hi Rashmi does it look correct in our visualization tools? If so, you'll need to talk to the AFNI folks. cheers Bruce On Wed, 4 Apr 2012, Rashmi Singh wrote: Hello,  I converted the aseg. mgz files to nii format and created a hippcampal mask with 3dcalc. Using AFNI I opened the