[Freesurfer] Hippocampal Subfield Segmentation with a T2: Warnings in the log file

External Email - Use Caution Hi all, I recently ran the hippocampal subfield segmentation script with a T2 scan. The subfield outputs make sense, however, when I was reviewing the log, I noticed this warning: makeIsotropic WARNING: not different enough, won't reslice! I also n

Re: [Freesurfer] Hippocampal Subfield segmentation problem - Matlab exits due to fatal error

Hi again, Georgia. RAM is definitely not the problem. Andrew: do you know what this could be? Cheers, Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Nov 18, 2021, at 15:55, Georgia Kapizioni mailto:geo.kapizi...@gmail.com>> wrot

Re: [Freesurfer] Hippocampal Subfield segmentation problem - Matlab exits due to fatal error

External Email - Use Caution Actually the same error occurs with thalamus segmentation also. I made the change you suggested on resolution at the segmentHA_T1.sh (yet I was not allowed to make the change on the initial file so I created a new one) and now when I run the command

Re: [Freesurfer] Hippocampal Subfield segmentation problem - Matlab exits due to fatal error

External Email - Use Caution Thank you so much for your reply Eugenio. I have 16 GB of RAM. Do you think this would be a problem? Thanks again, Georgia > On 18 Nov 2021, at 10:04 PM, Georgia Kapizioni > wrote: > > Dear Freesurfer experts, > > I am trying to run hippocampal

Re: [Freesurfer] Hippocampal Subfield segmentation problem - Matlab exits due to fatal error

Hi Georgia, How much RAM memory does your computer have? Is it possible that you ran out of it? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 18 Nov 2021, at 15:04, Georgia Kapizioni mailto:geo.kapizi...@gmail.

Re: [Freesurfer] hippocampal subfield segmentation with DCM

Hi Wei, You need to convert to nifti first, but you can do that with mri_convert: mri_convert ADNI_002_S_0295_MR_Axial_T2-Star__br_raw_20110602125226394_36_S110471_I238619.dcm. ADNI_002_S_0295_MR_Axial_T2-Star__br_raw_20110602125226394_36_S110471_I238619.nii.gz Cheers, /Eugenio Juan Eugeni

[Freesurfer] hippocampal subfield segmentation with DCM

External Email - Use Caution Hi, FreeSurfer experts I'm wondering if there is a way to do hippocampal subfield segmentation with T2 DCM images, instead of NifTi. like this ADNI_002_S_0295_MR_Axial_T2-Star__br_raw_20110602125226394_36_S110471_I238619.dcm Best, Wei __

Re: [Freesurfer] Hippocampal subfield segmentation

list Subject: Re: [Freesurfer] Hippocampal subfield segmentation External Email - Use Caution Hi, Dr. Iglesias Gonzalez Here is the full log, Thanks Best, Wei On Mon, Mar 1, 2021 at 10:33 PM Iglesias Gonzalez, Juan E. mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote: Dear We

Re: [Freesurfer] Hippocampal subfield segmentation

research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Monday, March 1, 2021 at 21:14 > *To: *Freesurfer support list > *Subject: *[Freesurfer] Hippocampal subfield segmentation > > > > *External Email - Use Caution* > > Hi, Freesur

Re: [Freesurfer] Hippocampal subfield segmentation

support list Subject: [Freesurfer] Hippocampal subfield segmentation External Email - Use Caution Hi, Freesurfer expert I tried Hippocampal subfield segmentation with an additional T2 scan by using FS7.1.0 Here is the log error massage Attempted to access cropping(1); index out of

[Freesurfer] Hippocampal subfield segmentation

External Email - Use Caution Hi, Freesurfer expert I tried Hippocampal subfield segmentation with an additional T2 scan by using FS7.1.0 Here is the log error massage Attempted to access cropping(1); index out of bounds because numel(cropping)=0. Error in applyCropping (line 7)

Re: [Freesurfer] Hippocampal subfield segmentation by T2 scan

External Email - Use Caution Hi Wei, I'm not one of the developers but std::bad_alloc probably means you ran out of memory, so it would be beneficial to the developers if you could include the details like - which version of FreeSurfer you're running, - how much memory that lin

[Freesurfer] Hippocampal subfield segmentation by T2 scan

External Email - Use Caution Hi, dear Freesurfer team I used sagittal T1(MPRAGE-sag_T1w.nii.gz) to recon-all and did the hippo-subfield segmentation on T1, but when I tried to use the additional scan by segmentHA_T2.sh : segmentHA_T2.sh sub-AVP14352 /home/weishao/sub-AVP14352/Ses

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

Reply-To: FS Help Date: Wednesday, April 8, 2020 at 11:26 PM To: FS Help Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error External Email - Use Caution Hello! So I have installed the latest Java, reinstalled the Runtime following the instructions on the Freesurfer we

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

t; Cheers, > > /Eugenio > > > > > > Juan Eugenio Iglesias > > Senior research fellow > > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuro

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

S Help Cc: "Hoopes, Andrew" Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error Uuuummm this is a tough one. Any ideas, Andrew? Maybe updating java? Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From:

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

ience" Reply-To: Freesurfer support list Date: Tuesday, March 31, 2020 at 17:59 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error External Email - Use Caution Hello Eugenio, No I wasn't! When I first tried to run the subfields I wa

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

n behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list > *Date: *Saturday, March 28, 2020 at 02:07 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocamp

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

t;Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" Reply-To: Freesurfer support list Date: Saturday, March 28, 2020 at 02:07 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error External Email - U

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

gt; > CMIC (UCL), MGH (HMS) and CSAIL (MIT) > > http://www.jeiglesias.com > > > > > > > > *From: * on behalf of "Lab of > Autism and Developmental Neuroscience, Lab of Autism and Developmental > Neuroscience" > *Reply-To: *Freesurfer support list

Re: [Freesurfer] Hippocampal Subfield Segmentation Error

://www.jeiglesias.com From: on behalf of "Lab of Autism and Developmental Neuroscience, Lab of Autism and Developmental Neuroscience" Reply-To: Freesurfer support list Date: Saturday, March 21, 2020 at 23:33 To: Freesurfer support list Subject: [Freesurfer] Hippocampal Subfield Segmenta

[Freesurfer] Hippocampal Subfield Segmentation Error

External Email - Use Caution Dear Freesurfer experts, I am having a problem with hippocampal subfield segmentation. The issue appears to be related to JavaVM - after I run the code: recon-all -s (subject ID) -hippocampal-subfields-T1 This is the error: JavaVM: Failed to load JVM:

Re: [Freesurfer] hippocampal subfield segmentation - values for whole subfields

Kaixo, Teresa. Yes, you would simply sum CA1-body + C1-head to get what used to be CA1 in FreeSurfer 6.0. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On 2/18/20, 05:57, "freesurfer-boun...@nmr.mgh.harvard.e

[Freesurfer] hippocampal subfield segmentation - values for whole subfields

External Email - Use Caution Hello FreeSurfer Developers, I am trying to use the Hippocampal subfields tool (https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala) to extract the stats of each subfield. On version v21 I obtain the stats for the subdi

Re: [Freesurfer] hippocampal subfield segmentation question

External Email - Use Caution Dear Eugenio, Thank you for the quick help. Best, Gabor ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] hippocampal subfield segmentation question

January 2020 at 20:43 To: freesurfer Subject: [Freesurfer] hippocampal subfield segmentation question External Email - Use Caution We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm inplane

[Freesurfer] hippocampal subfield segmentation question

External Email - Use Caution We have a sagittal 1 mm isotropic whole-brain 3D T1 mprage (morphometry protocol suggested on Freesurfer's page) and a coronal anisotropic (0.4mm inplane, 2mm thickness, similar to ADNI protocol) T2 measurement acquired perpendicular to the hippocampus

[Freesurfer] hippocampal subfield segmentation input mask?

External Email - Use Caution Dear FreeSurfer list, I'm wondering if there is any way to input different starting segmentations for the hippocampus into the hippocampal subfield segmentation? We've got a hippocampus specific segmentation algorithm which we'd like to try as inpu

Re: [Freesurfer] hippocampal subfield segmentation

freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Tuesday, August 21, 2018 3:17:15 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation External Email - Use Caution Hi Ryan, Is it possible that you'r

Re: [Freesurfer] hippocampal subfield segmentation

urfer] hippocampal subfield segmentation External Email - Use Caution Hello FreeSurfer users, I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRu

[Freesurfer] hippocampal subfield segmentation

External Email - Use Caution Hello FreeSurfer users, I want to segment hippocampal subfields, but did not have much luck running it. I downloaded the matlab compiler runtime according to this: https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime. Now, there is a directory ca

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

ay, May 31, 2018 8:37:44 PM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution My freesurfer home is /opt/freesurfer-6.0.0 which contains all the necessary freesurfer binaries, .sh files etc in order for fre

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

...@nmr.mgh.harvard.edu < >> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude < >> miracoo...@gmail.com> >> *Sent:* Wednesday, May 30, 2018 9:21:19 PM >> *To:* Freesurfer support list >> >> *Subject:* Re: [Freesurfer] hippocampal s

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

http://cmictig.cs.ucl.ac.uk/ > > > -- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of miracle ozzoude < > miracoo...@gmail.com> > *Sent:* Wednesday, May 30, 2018 9:21:19 PM > *

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

t: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Thanks. So I changed it to " export FREESURFER_HOME=/opt/freesurfer-6.0.0; source $FREESURFER_HOME/freesurfer/SetUpFreeSurfer.sh" (based on printenv). However, when i tried to

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

.ac.uk/ > > > > > > *From: * on behalf of miracle > ozzoude > *Reply-To: *Freesurfer support list > *Date: *Wednesday, 30 May 2018 at 18:57 > > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] hippocampal subfield segmentation error > (fsv6.0) > >

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

list Date: Wednesday, 30 May 2018 at 18:57 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Yes, because I processed all my subjects with v6.0 without any issue. When i type "printenv FREESURFER_HOME&

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

; > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of mira

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Hello, I checked and my sources.sh is located in /opt/freesurfer-6.0.0/freesurfer/sources.sh not /opt/freesurfer-6.0.0/sources.sh. I opened the kvlAutoCropt file and it

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

h mixing versions. > > What exact version are you using? > > Cheers, > > /Eugenio > > > > -- > > Juan Eugenio Iglesias > > ERC Senior Research Fellow > > Centre for Medical Image Computing (CMIC) > > University College London > > http:/

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

:46 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0) External Email - Use Caution Hello Eugenio, Thanks for the response. All my processing was done with FreeSurfer v6.0 although, we have version 5.3 installed on the server too. I

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

.uk/ > > > > > > *From: * on behalf of miracle > ozzoude > *Reply-To: *Freesurfer support list > *Date: *Wednesday, 30 May 2018 at 16:11 > *To: *Douglas N Greve > *Subject: *[Freesurfer] hippocampal subfield segmentation error (fsv6.0) > > > > *

Re: [Freesurfer] hippocampal subfield segmentation error (fsv6.0)

Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of miracle ozzoude Reply-To: Freesurfer support list Date: Wednesday, 30 May 2018 at 16:11 To: Douglas N Greve Subject: [Freesurfer] hippocampal subfield segmentation error

[Freesurfer] hippocampal subfield segmentation error (fsv6.0)

External Email - Use Caution Hello, I am using v6.0 installed on a linux server (via PUTTY) to segment hippocampal subfields. I downloaded the runtime from this link ( https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime) and followed the instructions on how to install it ( it

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.

Re: [Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hi Ryan, This is weird! I am safely assuming that you sourced FreeSurfer, etc? What was the command you ran? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeigle

[Freesurfer] Hippocampal subfield segmentation error: kvlAutoCrop.bin: command not found

External Email - Use Caution Hello FreeSurfer users, I am trying to run hippocampal subfield segmentation on our subjects on FreeSurfer version 6.0. Unfortunately, I was not able to get very far. I got an error relatively early: /netopt/rhel7/versions/freesurfer/freesurfer-6.0.

Re: [Freesurfer] Hippocampal subfield segmentation with T1 and T2

: Thursday, January 18, 2018 10:59:45 PM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampal subfield segmentation with T1 and T2 Hi all, I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run re

[Freesurfer] Hippocampal subfield segmentation with T1 and T2

Hi all, I've been trying to run the hippocampal subfield segmentation with T1 and T2 images, and haven't had much luck. I had previously run recon-all on all my scans in v5.3, but testing on one subject I re-ran recon-all with the additional T2 scan, and that seems to have run fine. However, when

Re: [Freesurfer] Hippocampal subfield segmentation error

ias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of "Md. Mamun > Al-Amin" > *Reply-To: *Freesurfer support list > *Date: *Sunday, 17 September 2017 at 03:46 > *To: *Freesurfer support list > *Subject: *Re: [Freesurfer] Hippocampal subfi

Re: [Freesurfer] Hippocampal subfield segmentation error

rfer support list Date: Sunday, 17 September 2017 at 03:46 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfield segmentation error Hi Eugenio Thanks for your attention. I solved this problem today. I found two JAVA versions in my macbook (Library/Java/JavaVirtualMach

Re: [Freesurfer] Hippocampal subfield segmentation error

; University College London > > http://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of "Md. Mamun > Al-Amin" > *Reply-To: *Freesurfer support list > *Date: *Friday, 15 September 2017 at 00:54 > *To: *Freesurfe

Re: [Freesurfer] Hippocampal subfield segmentation error

ot;Md. Mamun Al-Amin" Reply-To: Freesurfer support list Date: Friday, 15 September 2017 at 00:54 To: Freesurfer support list Subject: [Freesurfer] Hippocampal subfield segmentation error Dear Experts I have been experiencing a problem while running the following command segmentHA_T1.sh subject

[Freesurfer] Hippocampal subfield segmentation error

Dear Experts I have been experiencing a problem while running the following command *segmentHA_T1.sh subject_name* The program exits with the following error "MATLAB is exiting because of fatal error /Applications/freesurfer-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 39: 660 Ki

Re: [Freesurfer] Hippocampal subfield segmentation problem

Dear Artyom, You’re probably running out of RAM memory in those few cases. How much RAM do you have? 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 19 May 2017, at

[Freesurfer] Hippocampal subfield segmentation problem

Dear experts, I am running running hippocampal subfield segmentation using the most recent version of the FSv6.0 on LinuxMint 17.3 Rosa. For some (~ 25%, but not all) participants I did not get the subfields. I have later realized that although segmentation finished with out errors, I got the

Re: [Freesurfer] Hippocampal subfield segmentation, file content

Hi Nina, I’m very glad to hear that the segmentations look satisfactory :-) The ?h.hippoSfLabel.v10.mgz files already have that information; they are label volumes (FreeView assigns colors to the labels for visualization). The lookup table can be found in $FREESURFER_HOME/FreeSurferColorLUT.txt

[Freesurfer] Hippocampal subfield segmentation, file content

Hi All, I have made a hippocampal subfield segmentation using FreeSurfer version 6.0 with multispectral segmentation settings, and have both labels for the right and left hippocampus. The segmentations look very nice when viewed with freeview, so all good. Now, my problem is the file content.

Re: [Freesurfer] Hippocampal subfield segmentation "error" with T1 image

Hi, Perfect, thank you for the quick response! Best, Gustav On 2017-02-10 14:37, Iglesias Gonzalez, Eugenio wrote: Hi Gustav, No problem at all (ingen fara!). The idea is that, when our new joint atlas of the hippocampal subfields and amygdala nuclei is ready to be released, we’ll just need t

Re: [Freesurfer] Hippocampal subfield segmentation "error" with T1 image

Hi Gustav, No problem at all (ingen fara!). The idea is that, when our new joint atlas of the hippocampal subfields and amygdala nuclei is ready to be released, we’ll just need to replace the atlas files, without having to touch the code. It was my fault not to wrap that move command inside an I

Re: [Freesurfer] Hippocampal subfield segmentation in FS 6.0

researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer From: "Sarah Lancaster" To: "Freesurfer support list" Sent: Wednesday, February 17, 2016 3:39:16 PM Subject: [Freesurfer] Hippocampal subfield segment

[Freesurfer] Hippocampal subfield segmentation in FS 6.0

Hi all, We are running hippocampal subfield segmentations on about 300 subjects. We initially ran recon-all using FreeSurfer 5.3, but we used the new FreeSurfer 6.0 method for the hippocampal subfields. Will this cause problems in our analysis? Should we run them through recon-all again with 6.

Re: [Freesurfer] hippocampal subfield segmentation

Hi Mike, We have found that the volumes obtained by summing the subfield volumes discriminates a bit better between controls and AD subjects than the standard FS hippocampal volumes. Hope this helps, Koen On Tue, Apr 15, 2014 at 7:11 PM, Mike Strupp-Levitsky wrote: > To whom it may concern, >

Re: [Freesurfer] hippocampal subfield segmentation

To whom it may concern, I'm writing in regard to the thread below about using the sum of the hippocampal subfield volumes (excluding the hippocampal fissure). I'm finding that they are moderate-highly correlated with the hippocampal volumes from ASEG (~.75-.85). Do you have a sense of which of

Re: [Freesurfer] Hippocampal Subfield Segmentation

Dear Sierra, there's no direct correspondence between these subfields and head / body. If you want, you could create a geometric rule to subdivide the hippocampus into head / body / tail, e.g., by creating a coordinate system based on the major axis of the hippocampal shape. Kind regards, Eugenio

[Freesurfer] Hippocampal Subfield Segmentation

Hi everyone, In using Van Leemput's -hippo-subfields flag as part of the recon-all script to obtain hippocampal subfield volumes, my lab has determined that larger subfields are more relevant for our purposes clinically/surgically. Is there a way to group the fimbria/CA1/2,3/4,DG/presubiculum/s

Re: [Freesurfer] Hippocampal subfield segmentation paused

*Cc:* "freesurfer@nmr.mgh.harvard.edu" *Sent:* Tuesday, October 1, 2013 4:37 PM *Subject:* Re: [Freesurfer] Hippocampal subfield segmentation paused Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentat

Re: [Freesurfer] Hippocampal subfield segmentation paused

urfer@nmr.mgh.harvard.edu" Sent: Tuesday, October 1, 2013 4:37 PM Subject: Re: [Freesurfer] Hippocampal subfield segmentation paused Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentation based only on t

Re: [Freesurfer] Hippocampal subfield segmentation paused

Hi Irene, two things: 1. Can you please send us the log files of the recon? 2. The command you executed will compute the subfield segmentation based only on the T1, not the high-res T2. Cheers, /Eugenio On 10/01/2013 04:30 PM, Irene Lee wrote: Hi, there, I am running the hippocampal subfield

[Freesurfer] Hippocampal subfield segmentation paused

Hi, there, I am running the hippocampal subfield segmentation on a high resolution T2 data that only covers the bilateral hippocampus and nearby temporal lobe areas.  Following the instruction on this webpage: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I used the com

Re: [Freesurfer] Hippocampal Subfield Segmentation

Hi Sierra, the hippocampal subfield segmentation is computed using a separate model, so it doesn't agree perfectly with the hippocampal mask in aseg.mgz. In fact, the volume estimates tend to be a bit smaller (but highly correlated). Cheers, /Eugenio On 09/30/2013 10:42 AM, Germeyan, Sierra (NI

[Freesurfer] Hippocampal Subfield Segmentation

Hi everyone, After running -hippo-subfields, I converted the voxel output of -hippo-subfields to mm^3 based on the instructions given here: https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-June/031188.html. Then I summed the volumes for all of the subfields (assuming that this would

Re: [Freesurfer] hippocampal subfield segmentation

Title Automated segmentation of hippocampal subfields from ultra‐high resolution in vivo MRI Authors Koen Van Leemput, Akram Bakkour, Thomas Benner, Graham Wiggins, Lawrence L Wald, Jean Augustinack, Bradford C Dickerson, Polina Golland, Bruce Fischl Year 2009 Hippocampus Volume 19 Issue 6 Pages 5

Re: [Freesurfer] hippocampal subfield segmentation

Thank you for your response. Would you suggest a reference I can refer to? 2013/6/4 Juan Eugenio Iglesias > I would probably leave out the fissure, but not the fimbria... > Cheers, > /Eugenio > > On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: > > Hi guys! > > I have a dataset includ

Re: [Freesurfer] hippocampal subfield segmentation

I would probably leave out the fissure, but not the fimbria... Cheers, /Eugenio On Tue, 2013-06-04 at 14:33 +0200, Claudia Dacquino wrote: > Hi guys! > I have a dataset including hippocampal subfields obtained through the > -hippo-subfields flag. I want to have a measure of total hippo volume > an

[Freesurfer] hippocampal subfield segmentation

Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or shoul

Re: [Freesurfer] hippocampal subfield segmentation

Hi Antonella, Just run recon-all with the flag "-hippo-subfields" but without the flag "-all" (otherwise you'll be rerunning a lot of stuff you do not need to rerun): DO: recon-all -s bert -hippo-subfields DON'T DO: recon-all -s bert -all -hippo-subfields Kind regards, /Eugenio On Mon, 2012-12-03

[Freesurfer] hippocampal subfield segmentation

Dear FS team, I would like to know if there is any options to get the hippocampal subfield segmentation so I can get the volume for each segmentation if I was running only recon-all for all my subjects or I need to re-run recon-all but with a hippocampal subfield segmentation option this tim

[Freesurfer] hippocampal subfield segmentation

Hi Freesurfer community, A quick question, how long takes to run the hippocampal subfield segmentation for a subject that has already run the typical recon-all pipeline? Thank you, -- -- *Carolina Valencia M * ___ Freesurfer mailing list Freesurfer@nm

[Freesurfer] Hippocampal subfield segmentation error

Hello,I got the following error in one of my subjects when running hippocampal subfields segmentation (only for the left hemisphere). Could you help me to solve this problem?maximalDeformation: 75.1793 Transforming mesh Done transforming mesh Rasterizing Levenberg-Marquardt... number

[Freesurfer] hippocampal subfield segmentation

Dear Van Leemput & Freesurfers, I've been working with the GEMS tool for hippocampal subfields segmentation and have a question I would like to ask you. I've noticed that the CA1 sector appears to be quite small compared to other subfields (CA2-3 seems to be the largest), while previous studies s

[Freesurfer] hippocampal subfield segmentation

Dear Van Leemput & Freesurfers, I've been working with the GEMS tool for hippocampal subfields segmentation and have a question I would like to ask you. I've noticed that the CA1 sector appears to be quite small compared to other subfields (CA2-3 seems to be the largest), while previous studies s

Re: [Freesurfer] Hippocampal subfield segmentation

Thanks. Does freeview use same approach as what Koen described? Look like both ways need upsampling nu to 0.5x0.5x0.5. Wayne On 12/07/11 10:29 AM, "Bruce Fischl" wrote: > it of course resamples for overlay, but it doesn't downsample - just uses > the vox2ras matrices from the two volumes to co

Re: [Freesurfer] Hippocampal subfield segmentation

it of course resamples for overlay, but it doesn't downsample - just uses the vox2ras matrices from the two volumes to compute a common space On Tue, 12 Jul 2011, Wayne Su wrote: > Thank you Koen. We're investigating the VR Space volume in each hippocampal > subfield. Your suggestion is just wha

Re: [Freesurfer] Hippocampal subfield segmentation

Thank you Koen. We're investigating the VR Space volume in each hippocampal subfield. Your suggestion is just what I'm looking for, very helpful. Yes, I can use freeview to display them as an overlay. don't how freeview achieves that. Are you sure no resampling there for the command: freeview nu.m

Re: [Freesurfer] Hippocampal subfield segmentation

Or you could use freeview to display them as an overlay without any resampling. What is it you are trying to do? On Jul 12, 2011, at 5:56 AM, Koen Van Leemput wrote: > Hi Wayne, > > You're right: It will be difficult to somehow shoehorn the probability > images with voxel size 0.5mm isotropic

Re: [Freesurfer] Hippocampal subfield segmentation

Hi Wayne, You're right: It will be difficult to somehow shoehorn the probability images with voxel size 0.5mm isotropic into the orginal 1mm isotropic FreeSurfer volumes. The other way around, by resampling the 1mm input image onto the correct 0.5mm grid is easy, though: kvlUpsample nu.mgz 2 kvl

Re: [Freesurfer] Hippocampal subfield segmentation

Hi Koen, Look like the outputs (posterior_*.mgz) are probability kind of images. How can I transfer them back into 1x1x1 mm^3 FS space? Maybe merge them into one image without overlapping? Or maybe transfer my own image into this 0.5x0.5x0.5 mm^3 space. How can I achieve this? Thanks, Wayne On 0

Re: [Freesurfer] Hippocampal subfield segmentation

Hi Tricia, Yes, that summarizes it neatly. :-) Koen On Mon, Jul 4, 2011 at 10:44 PM, Tricia Merkley wrote: > Hi, > > I understand that the models for the hippocampal subfield segmentation were > created using high resolution MRI scans. But it sounds like this procedure > can be used for scan

[Freesurfer] Hippocampal subfield segmentation

Hi, I understand that the models for the hippocampal subfield segmentation were created using high resolution MRI scans.  But it sounds like this procedure can be used for scans with 1mm ^3 resolution, right?  The resulting values would just need to be divided by 8 in order to get the subfield