Re: [Freesurfer] Hippocampus and amygdala segmentation

...@nmr.mgh.harvard.edu on behalf of Miguel Ángel Rivas Fernández Date: Friday, February 21, 2025 at 1:18 AM To: Freesurfer support list Subject: [Freesurfer] Hippocampus and amygdala segmentation External Email - Use Caution Dear Eugenio, My name is Miguel. I am currently processing data of the ABCD

[Freesurfer] Hippocampus and amygdala segmentation

External Email - Use Caution Dear Eugenio, My name is Miguel. I am currently processing data of the ABCD Study using FreeSurfer. In our pipeline, we also include the specific FreeSurfer segmentations for the hippocampus and amygdala. As an additional step, we would like to use the

Re: [Freesurfer] Hippocampus Subfields Stats (FreeSurfer v7.3.2)

Silva, Narlon Date: Tuesday, September 10, 2024 at 12:12 PM To: Freesurfer support list Subject: [Freesurfer] Hippocampus Subfields Stats (FreeSurfer v7.3.2) Hi there, I have searched the archive and couldn't find information relating to this issue. I am running longitudinal analysis i

Re: [Freesurfer] Hippocampus subfield LUT

Look in $FREESURFER/FreeSurferLUT.txt This has those indices (and a lot more). If you want just the hippo SF indices, you can run something like mri_segstats --seg hipposf.mgz --ctab-default --sum sum.dat The indices will be in sum.dat On 5/14/2024 11:04 AM, karl landheer wrote: Exter

[Freesurfer] Hippocampus subfield LUT

External Email - Use Caution Hello, I am looking for the LUT which converts the indices in images like lh.hippoAmygLabels-T.v22.mgz to region name. Is this available anywhere? I can’t find it ___ Freesurfer mailing list Freesurfer@nmr.mgh

Re: [Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash

9, 2023 8:21 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash External Email - Use Caution Hi there, I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am tr

Re: [Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash

External Email - Use Caution Please try using the Matlab runtime environment which can be installed directly into the freesurfer tree via a script we provide.  The runtime environment is free and requires no paid for Matlab license (since it does not include the Matlab compiler)

[Freesurfer] Hippocampus Segmentation Troubleshoot - Matlab crash

External Email - Use Caution Hi there, I am a Master's student who is looking to segment the hippocampus and analyze diffusion data of the segments. I am trying to utilize the segmentation function with this command: segmentHA_T1.sh subj01 But I am met with this error saying that

Re: [Freesurfer] FreeSurfer Hippocampus Segmentation Question

are you talking about the whole hippo seg? That will have some WM in it. You can also try the hippo subfield segmentation which will give you a more refined segmentation separating GM and WM. On 11/7/2022 11:16 AM, Jun Yeon Won wrote: External Email - Use Caution Dear Freesurfer expe

[Freesurfer] FreeSurfer Hippocampus Segmentation Question

External Email - Use Caution Dear Freesurfer experts, I have a question about hippocampal segmentation. For the hippocampal mask after completing recon-all, is it purely gray matter or does it also include some aspects of white matter and others? Please advise. Best, JW _

Re: [Freesurfer] Hippocampus subfield segmentation

External Email - Use Caution Hello, Thank you for the quick response. Yes, I have kind of done that. But just wanted a little more clarification if I should use GLM further. Thanks for the info. On Thu, Jun 24, 2021 at 7:41 PM Iglesias Gonzalez, Juan E. < jiglesiasgonza...@mg

Re: [Freesurfer] Hippocampus subfield segmentation

Dear Ishi, At this point, you have a bunch of volumes for each subjects (in hippo test.txt), not maps. You can analyze them with your favorite statistical software ;-) Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On J

[Freesurfer] Hippocampus subfield segmentation

External Email - Use Caution Hello FS experts, I have performed hippocampus subfield segmentation on my T1 scans. I also gathered the volume from all my analyzed subjects through the following command - quantifyHippocampalSubfields.sh T1 hippotest.txt Now I want to perform sta

Re: [Freesurfer] Hippocampus ROI

You could also run recon-all on the mni152 template, then run the hippo/amyg seg on the output. It will give you the same bad segmentation:) On 5/20/2021 9:21 AM, Iglesias Gonzalez, Juan E. wrote: Hi Jessica, There’s no direct way of doing this, since the atlas lives it its own space and ther

Re: [Freesurfer] Hippocampus ROI

Hi Jessica, There’s no direct way of doing this, since the atlas lives it its own space and there’s no intensity volume you can deform to MNI, only probabilities. Having said that, you could 1. segment all your subjects with the hippocampal module, 2. register the subjects to MNI, 3. Deform the

[Freesurfer] Hippocampus ROI

External Email - Use Caution Dear FreeSurfer experts, I am trying to create a hippocampus ROI in FSL (MNI 152_2mm brain space) from the FreeSurfer 7.0 hippocampal/amygdala segmentation. How do I create this ROI? Best, Jessica ___ Free

Re: [Freesurfer] Hippocampus segmentHA_T1.sh

lto:ws...@research.baycrest.org>> > Reply-To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>> > Date: Friday, April 23, 2021 at 12:04 > To: Freesurfer support list <mailto:freesurfer@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] Hippocampus segmentHA_T1.

Re: [Freesurfer] Hippocampus segmentHA_T1.sh

: Freesurfer support list Subject: Re: [Freesurfer] Hippocampus segmentHA_T1.sh External Email - Use Caution Hi, E [weishao@gra-login1 01]$ find . -name "talairach.xfm" ./mri/transforms/talairach.xfm module load freesurfer/7.1.0 export SUBJECTS_DIR=/home/weishao/scratch/BART segme

Re: [Freesurfer] Hippocampus segmentHA_T1.sh

qaLDKyFd02VgXiETYyw2tNFfN3h2cuLMizK/http%3A%2F%2Fwww.jeiglesias.com > > > > > > > > *From: * on behalf of Wei Shao < > ws...@research.baycrest.org> > *Reply-To: *Freesurfer support list > *Date: *Friday, April 23, 2021 at 11:05 > *To: *Freesurfer supp

Re: [Freesurfer] Hippocampus segmentHA_T1.sh

, April 23, 2021 at 11:05 To: Freesurfer support list Subject: [Freesurfer] Hippocampus segmentHA_T1.sh External Email - Use Caution Hello, Dear FreeSurfer expert I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz

[Freesurfer] Hippocampus segmentHA_T1.sh

External Email - Use Caution Hello, Dear FreeSurfer expert I tried to use segmentHA_T1.sh for the hippocampus subfields, However, here is the log cannot find the wmparc.mgz or norm.mgz or talairach.xfm for the subject. Has the subject been procesed with recon-all? But the wmparc.

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

...@nmr.mgh.harvard.edu on behalf of Ishi Tandon AIB, Jaipur Date: Thursday, March 4, 2021 at 1:17 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS External Email - Use Caution Yes, the same error occurred again. It

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hello Ishi, After reviewing this thread, I made a *.deb installer from the 7.1.1 release.  I will send a download link to your private email so you can try it if you like.  You will need sudo privileges to run it.  If you try it, I suggest you first

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Yes, the same error occurred again. It would be great if someone from the dev team could help me resolve it. On Thu, Mar 4, 2021 at 11:29 AM Horsng Junn wrote: > External Email - Use Caution > > You mean the following error occurred again?

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution You mean the following error occurred again? libncurses.so.5: cannot open shared object file: No such file or directory Sorry but I ran out of ideas. Could anyone from the FreeSurfer dev team chime in? Please delete the file you just created with the

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Thanks alot. That seems to have executed without any errors. But segmentHA_T1.sh

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Then installing libncurses5-dev doesn't seem like the solution we've been seeking after all. Could you try this instead? sudo ln -s /usr/lib/x86_64-linux-gnu/libncurses.so.6.2 /usr/lib/x86_64-linux-gnu/libncurses.so.5 Regards, Horsng > On Mar 4, 2

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hi Ishi, The results suggest that libncurses5-dev isn't installed at all. (Listed files are all from the default libncurses 6) In your previous mail you said that: >> Also, I have tried sudo apt-get install libncurses5-dev. But that doesn't >> seem

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hi Ishi, Following are what I gathered: - You're running Freesurfer 7.1.1 on an ubuntu 20.04 box - Ubuntu 20.04 has libncurses 6 installed as default - Freesurfer 7.1.1 is linked against libncurses 5 - So previously you were advised to install libncur

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hello experts, With reference to my previous email, I am attaching the log file of segmentHA_T1.sh

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hello, Thanks for those suggestions. I already seem to have modified my bashrc with the same command. But I think running as root was a problem. But that's weird as earlier none of the Fs commands were executed without root. But now that seems to wor

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution And you seem to be running FreeSurfer as root. Since that could complicate matters, could you run it as a normal user? Best, Horsng > On Feb 24, 2021, at 9:36 AM, Horsng Junn wrote: > > Hi Ishi, > > I'm actually not a FreeSurfer developer and this

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hi Ishi, I'm actually not a FreeSurfer developer and this question seems beyond me, but my googling leads to this page: https://secure-web.cisco.com/1tvdf5d8d-n_4_yvtpnDy1tW-h4qQnq2_ZkoCU5wZomtFsWZ-CDUCe9hdZND8pvg-6Zs954WFqOc9uonDsuGXWWb2s4TMIIXYq9XIL

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hi Ishi, You apparently omitted an "n": it must be libncurses5-dev (please note the n after lib). And please try to keep previous correspondences intact, as otherwise the devs must hunt the mail archive for the detail. Best, Horsng > On Feb 23, 20

[Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

External Email - Use Caution Hello experts, In response to the previous email about matlab installation error while attempting to use hippocampal subfields. I tried the following command as suggested by you :- sudo apt-get install libcurses5-dev But I get the following error :-

Re: [Freesurfer] Hippocampus subfield segmentation error on Ubuntu 20.04.1 LTS

Hi Ishi, What FS version are you using? Can you try installing `apt-get install libncurses5-dev`? Andrew From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Ishi Tandon Date: Thursday, February 18, 2021 at 12:59 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Hippocampus

Re: [Freesurfer] Hippocampus {Disarmed}

Thank you OK, I can try From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, May 11, 2020 2:44 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampus {Disarmed} Can you get the coords by loading the

Re: [Freesurfer] Hippocampus {Disarmed}

. *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, May 11, 2020 2:25 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Hippocampus {Disarmed} And how do you want to define your voxel? As a

Re: [Freesurfer] Hippocampus {Disarmed}

: [Freesurfer] Hippocampus {Disarmed} And how do you want to define your voxel? As a bounding box around a particular structure (or structures)? Which ones? On 5/11/2020 2:12 PM, Del Re, Elisabetta wrote: Hi Douglas, basically yes. Thank you so much, Elisabetta From

Re: [Freesurfer] Hippocampus {Disarmed}

*From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve *Sent:* Monday, May 11, 2020 1:15 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Hippocampus {Disarmed} I'm still not sure what you are asking for. Do you want coordinates for you

Re: [Freesurfer] Hippocampus {Disarmed}

Hi Douglas, basically yes. Thank you so much, Elisabetta From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas N. Greve Sent: Monday, May 11, 2020 1:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampus {Disarmed} I&#

Re: [Freesurfer] Hippocampus {Disarmed}

E. *Sent:* Monday, May 11, 2020 12:18 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] Hippocampus Dera Elisabetta, Can you please give us some more detail on what you mean by “I am trying to translate the same subdivision to MRI acquisition for spectroscopy purposes.”? Cheers,

Re: [Freesurfer] Hippocampus {Disarmed}

tions From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Sent: Monday, May 11, 2020 12:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampus Dera Elisabetta, Can you please give us some more detail on what you mean by “I am tryi

Re: [Freesurfer] Hippocampus

From: on behalf of "Del Re, Elisabetta" Reply-To: Freesurfer support list Date: Monday, May 11, 2020 at 09:42 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Hippocampus Dear Freesurfer team, I have analyzed the anterior/posterior hippocampus successfully u

[Freesurfer] Hippocampus

Dear Freesurfer team, I have analyzed the anterior/posterior hippocampus successfully utilizing FS6.0. I am trying to translate the same subdivision to MRI acquisition for spectroscopy purposes. Do you have suggestions? Thank you very much, regards, Elisabetta _

Re: [Freesurfer] Hippocampus Subfields Segmentation

The file with HBT in the name. See https://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldsAndNucleiOfAmygdala On 5/6/2020 2:14 PM, Muhammad Naveed Iqbal Qureshi wrote: External Email - Use Caution Hi FreeSurfer experts, I preprocess my data with FreeSurfer v 6. After it I ran d

[Freesurfer] Hippocampus Subfields Segmentation

External Email - Use Caution Hi FreeSurfer experts, I preprocess my data with FreeSurfer v 6. After it I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I get the following output: # Hippocampal subfield volumes as created by segmentHA_T1

[Freesurfer] Hippocampus subfields ROI

External Email - Use Caution Hi FreeSurfer experts, I ran developmental version of freesurfer to get the hippocampus subfields ROI and volume. I can see in the hipposubfields.lh.T1.v21.stats and lh.hippoSfVolumes-T1.v21.txt fils with separate information for the head and tail vo

Re: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans

er support list > *Date: *Tuesday, April 7, 2020 at 06:26 > *To: *Freesurfer support list > *Subject: *[Freesurfer] hippocampus subfield segmentation using Siemen > and GE scans > > > > *External Email - Use Caution* > > Hi Freesurfer Community, &g

Re: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans

: Tuesday, April 7, 2020 at 06:26 To: Freesurfer support list Subject: [Freesurfer] hippocampus subfield segmentation using Siemen and GE scans External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view

[Freesurfer] hippocampus subfield segmentation using Siemen and GE scans

External Email - Use Caution Hi Freesurfer Community, I have run Hippocampus subfield segmentation using scans from GE and Siemens. The field of view (FOV) for GE and Siemens are different, with FOV of 8 and 9 respectively. Will this affect the analysis since they have different F

Re: [Freesurfer] Hippocampus subfields outputs missing

support list Date: Friday, 6 December 2019 at 13:44 To: Freesurfer maillist Subject: [Freesurfer] Hippocampus subfields outputs missing External Email - Use Caution Hi I ran the following command not the subject on HPC module load matlab/r2013a module load freesurfer/6.0.0 source

[Freesurfer] Hippocampus subfields outputs missing

External Email - Use Caution Hi I ran the following command not the subject on HPC module load matlab/r2013a module load freesurfer/6.0.0 source $FREESURFER_HOME/SetUpFreeSurfer.sh fixup_mni_paths recon-all -all -no-isrunning -s /hpf/projects/glongoni/ADHD-200/$file -subjid

Re: [Freesurfer] Hippocampus Subregion

tember 2019 at 07:35 To: freesurfer Subject: [Freesurfer] Hippocampus Subregion External Email - Use Caution Dear Freesurfer experts, I got the volume of hippocampal subregions by using the command - "recon-all -all -s bert -hippocampal-subfields-T1" in Free

[Freesurfer] Hippocampus Subregion

External Email - Use Caution Dear Freesurfer experts,                I got the volume of hippocampal subregions by using the command -  "recon-all -all -s bert -hippocampal-subfields-T1" in Freesurfer. How do I get the surface-level metrics of the hippocampal subregions (e.g.,

Re: [Freesurfer] hippocampus subfield division

of Yixin Ma Reply-To: Freesurfer support list Date: Monday, 11 February 2019 at 10:01 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] hippocampus subfield division External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about the hippo

[Freesurfer] hippocampus subfield division

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask about the hippocampus subfield division again. Last time, I gave you an example of the subject that I failed to run the hippocampal subfield division, and you told me that you were able to run the hippocampus s

Re: [Freesurfer] Hippocampus subfield division error

Medical School http://www.jeiglesias.com From: on behalf of Yixin Ma Reply-To: Freesurfer support list Date: Tuesday, 22 January 2019 at 10:09 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Hippocampus subfield division error External Email - Use Cau

Re: [Freesurfer] Hippocampus subfield division error

External Email - Use Caution Hi Dr. 00246.zip Iglesias I have the problem of hippocampus subfield division not working. You mentioned that I can upload one of the subjects as an example. I'm n

Re: [Freesurfer] Hippocampus subfield division error

Date: Friday, 18 January 2019 at 12:28 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Hippocampus subfield division error External Email - Use Caution Hi, The hippocampus subfields division problem happens on more than one subjects (~10). However, I have successfu

Re: [Freesurfer] Hippocampus subfield division error

External Email - Use Caution Hi, The hippocampus subfields division problem happens on more than one subjects (~10). However, I have successfully run it on one subject (which is a little earlier in time, before I failed to run recent 10 subjects). Thank you for your help. Best re

Re: [Freesurfer] Hippocampus subfield division error

: Friday, 18 January 2019 at 11:06 To: "freesurfer@nmr.mgh.harvard.edu" Subject: [Freesurfer] Hippocampus subfield division error External Email - Use Caution Hi FreeSurfer experts, I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0. I got an e

[Freesurfer] Hippocampus subfield division error

External Email - Use Caution Hi FreeSurfer experts, I'm writing to ask about the hippocampus subfields division in FreeSurfer 6.0. I got an error message as attached, could you please help me with which part might have gone wrong? This subject's other recon-all worked but not for

Re: [Freesurfer] HIPPOCAMPUS AND AMYGDALA SEGMENTATION - Invalid MEX-file

External Email - Use Caution Hello Alba, As of Mac OS 10.11, El Capitan, DYLD_LIBRARY_PATH and DYLD_FALLBACK_LIBRARY_PATH are ignored as environment variables at run time.  Same for all subsequent releases: Sierra = 10.12; High Sierra = 10.13; Mojave = 10.14. You could try sett

[Freesurfer] HIPPOCAMPUS AND AMYGDALA SEGMENTATION - Invalid MEX-file

External Email - Use Caution Dear Freesurfer experts, We installed today (8 jan 2019) the last version of Freesurfer dev and the corresponding Runtime Matlab R2014b . We tried segmentHA_T1.sh with bert to check if it worked. We had a couple of errors related to an Invalid Mex-file

Re: [Freesurfer] Hippocampus cortical layers division

sorry, I don't think we have anything that will do what you want cheers Bruce On Tue, 18 Dec 2018, Yixin Ma wrote: External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cort

[Freesurfer] Hippocampus cortical layers division

External Email - Use Caution Hi Freesurfer experts, I'm writing to ask if you have any suggestions on generating cortical layers for hippocampus subfield cortical regions with the help of freesurfer. When generating cortical layers for other neocortex brain region, the surface fil

Re: [Freesurfer] hippocampus cortex surface

sorry, we don't have a hippo cortex analysis method On 12/05/2018 10:26 AM, Yixin Ma wrote: > > External Email - Use Caution > > Hi Freesurfer experts, > > After running the segmentation of hippocampus subfields, I'm wondering > if I can get the surface of the gray matter and white matter

[Freesurfer] hippocampus cortex surface

External Email - Use Caution Hi Freesurfer experts, After running the segmentation of hippocampus subfields, I'm wondering if I can get the surface of the gray matter and white matter of hippocampus in addition to subfields. My goal is to divide the hippocampus cortex into multip

Re: [Freesurfer] hippocampus subfields with T2

Alexopoulos, Dimitrios Sent: Thursday, August 30, 2018 9:38:50 PM To: Freesurfer support list Subject: [Freesurfer] hippocampus subfields with T2 External Email - Use Caution We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic T1-mprage and a 1mm isotropic T2

[Freesurfer] hippocampus subfields with T2

External Email - Use Caution We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic T1-mprage and a 1mm isotropic T2-space. Is it possible or even recommended to try and generate better hippocampal segmentation in fressurfer 6.0 using both the T1 and T2,

Re: [Freesurfer] hippocampus subfields and manual editing

External Email - Use Caution Hi Lara, A little trick you can do (it shouldn’t be too hard to implement in Matlab with the functions in $FREESURFER_HOME/matlab) For each subject: 1. make a copy of aseg.mgz 2. create a binary mask for your edited hippocampi. 3. in aseg.mgz, replace

[Freesurfer] hippocampus subfields and manual editing

External Email - Use Caution Hello, I am running an analysis of hippocampus volume on a set of T1-weighted scans with 1mm^3 isotropic resolution. Due to flow and other artifacts, a moderate degree of manual editing was required to correct the boundaries of each subject's hippo

[Freesurfer] Hippocampus subfields {Disarmed}

Hi Experts, I ran the segmentation of hippocampus in Freesurfer dev version. The left or right whole volume isn't equal to the sum of 12 subfields. But it is equal to the sum of the volume of tail, whole head and body. Why? I am looking forward to your reply. Thank you very much. Sincerely, Zh

Re: [Freesurfer] Hippocampus Subfield analysis error

Hi Andrew, thanks for your reply. Yes, I am using bash and my operating system is Mac OS X 10.9.5. Could you direct me how to set a path correctly? I ran recon_all fine. On Wed, Jan 24, 2018 at 1:14 PM, Hoopes, Andrew wrote: > Hi Hannah, > > > > What kind of environment are you running this in?

Re: [Freesurfer] Hippocampus Subfield analysis error

Hi Hannah, What kind of environment are you running this in? These errors make it seem like you do not have a PATH variable set at all. Are you using bash? and what operating system? best Andrew > On Jan 22, 2018, at 4:06 AM, Iglesias Gonzalez, Eugenio > wrote: > > Hi Hannah, > This seems

Re: [Freesurfer] Hippocampus Subfield analysis error

Hi Hannah, This seems like a more general problem with your PATH, but I’m sure Andrew (CCed) has a better idea of what might be going on. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cm

[Freesurfer] Hippocampus Subfield analysis error

Hi Freesurfer experts, I tried to do hippocampus subfield analysis but failed. I got this error message: #@# Hippocampal Subfields processing (T1 only) left Fri Jan 19 15:27:36 PST 2018 dirname: Command not found. pwd: Command not found. pwd: Command not found. /run_segmentSubjectT1_autoEstim

Re: [Freesurfer] Hippocampus subfield ROI

강준영 Reply-To: Freesurfer support list Date: Tuesday, 19 December 2017 at 10:10 To: Freesurfer support list Subject: [Freesurfer] Hippocampus subfield ROI Deer Freesurfer Experts. I'm currently working on hippocampus subfield parcellation in freesurfer version 6.0.0 In the previous ve

[Freesurfer] Hippocampus subfield ROI

Deer Freesurfer Experts. I'm currently working on hippocampus subfield parcellation in freesurfer version 6.0.0 In the previous version, freesurfer gave me CA1, CA3 and other subfields with separate mgz files so I could easily analyze them by AFNI separately. (make afni files for each subfields)

Re: [Freesurfer]  hippocampus subfields

Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of 郑凤莲 <13181786...@163.com> Reply-To: Freesurfer support list Date: Friday, 1 December 2017 at 12:55 To: Freesurfer support list Subject: Re: [Free

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, I am sorry for asking you question as this, but I really don't know how to do it? It seems that GLM is suitable for there are two groups or more. But I only have one group, If I want to get the line trend with eTIV corrected for the relationship between age and volume, what s

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, It's OK. Thank you very much for your reply ! I will find it in other way. Sincerely, Zheng At 2017-11-23 11:37:37, "Bruce Fischl" wrote: Sorry, I don’t remember. You can search on the wiki or maybe someone else will chime in Bruce On Nov 22, 2017, at 8:30 PM, 郑凤莲 <13181786...

Re: [Freesurfer]  hippocampus subfields

Sorry, I don’t remember. You can search on the wiki or maybe someone else will chime in Bruce > On Nov 22, 2017, at 8:30 PM, 郑凤莲 <13181786...@163.com> wrote: > > Hi Bruce, > > Could tell me which is the whole brain volume,please? I'm not sure which > is right. I need your help. > > Th

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Could tell me which is the whole brain volume,please? I'm not sure which is right. I need your help. Thanks very much. Zheng At 2017-11-22 11:07:36, "Bruce Fischl" wrote: >no, eTIV is the estimated volume of the intracranial vault, so it >included sulcal CSF. I think

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, There is aseg.stats. Is it brain segmentation volume? And in QDEC, I study the relationship between age and the cortical thickness, volume and surface area. The eTIV for volume and surface area should be set in Nuisance Factors, but for thickness, it's not need. Is right?

Re: [Freesurfer]  hippocampus subfields

no, eTIV is the estimated volume of the intracranial vault, so it included sulcal CSF. I think we include a whole brain volume in the aseg.stats file that you can use, although I don't remember what it's called cheers Bruce On Wed, 22 Nov 2017, 郑凤莲 wrote: Hi Bruce,     Thank you very much. I

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Thank you very much. I will try it. And I have another question. I also want to study the relation between age and the whole brain volume, gray matter volume and white matter volume. The whole brain volume is the same as eTIV, is right? Thanks, Zheng At 2017-11-22 10:29:4

Re: [Freesurfer]  hippocampus subfields

you would include it as a nuisance variable in the glm On Wed, 22 Nov 2017, 郑凤莲 wrote: Hi Bruce,      Thanks for your quick reply. These results are not correted by eTIV, If eTIV are corrected, I can only get the p value and scatter plot, I can't get the line trend. Do you know how to get t

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Thanks for your quick reply. These results are not correted by eTIV, If eTIV are corrected, I can only get the p value and scatter plot, I can't get the line trend. Do you know how to get the line trend with eTIV corrected as these results? Thanks, Zheng 在 2017-11-22

Re: [Freesurfer]  hippocampus subfields

is this eTIV corrected? I would look at some of the outliers and make sure that the segmentations are accurate. Certainly the trend is in the correct (and depressing) direction. cheers Bruce On Wed, 22 Nov 2017, 郑凤莲 wrote: Hi Bruce,     Thanks for your advice. There are a part of the result.

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Thanks for your advice. There are a part of the result. Blue color stands women, and Red color stands men. The number of the data is not enough large. Are they ok? May I use them in my paper? Thanks a lot ! Zheng At 2017-11-20 10:15:49, "Bruce Fischl" wrote: >Hi Z

Re: [Freesurfer]  hippocampus subfields

Hi Zheng I would scatter plot age vs. volume, coloring men and women differently (or different symbols) with and without eTIV correction to get an idea of what is going on cheers Bruce On Mon, 20 Nov 2017, 郑凤莲 wrote: Hi Bruce,     My data is loss from 35 to 40. But the uniform of sex is

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, My data is loss from 35 to 40. But the uniform of sex is not well from 40 to 55 and from 56 to 71. I did the correlation analysis between age and volume. I don't know how I can explain this problem. Thanks again. Sincerely, Zheng At 2017-11-20 09:35:45, "Bruce Fischl

Re: [Freesurfer]  hippocampus subfields

Hi Zheng how uniform is your distribution? I'm hardly an expert on this, but I wouldn't expect very large effects until you get into the older end of that range. Have you scatter plotted your data? Bruce On Mon, 20 Nov 2017, 郑凤莲 wrote: Hi Bruce,     Thank you for your help.     I have  5

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, Thank you for your help. I have 54 subjects, aged from 21 to 71 and only one group. I want to compare the change of hippocampus volume with age. The results before and after doing the correction for eTIV are the same. Where is wrong? Or if there is no error, how can I expla

Re: [Freesurfer]  hippocampus subfields

Hi Zheng yes, I see. Maybe the effect is smaller than you have the power to see, or there is no effect? You would need to give us more details for us to help. Are you correcting for eTIV? What measure are you comparing? cheers Bruce On Sun, 19 Nov 2017, 郑凤莲 wrote: Hi Bruce,      I am sorr

Re: [Freesurfer]  hippocampus subfields

Hi Bruce, I am sorry for this situation. In the first way, there was an statistical difference in left hippocampus, but no difference in right hippocampus. In the second way, there was both no statistical difference in left or right hippocampus. I don't know what causes this result

Re: [Freesurfer]  hippocampus subfields

Hi Zheng no difference between what and what? cheers Bruce On Fri, 17 Nov 2017, 郑凤莲 wrote: Hi professor,     I am using Freesurfer for DTI data. When I run 'mri_segstats',  I got the result that there was an obvious difference in left hippocampus, but no difference in right  hippocampus. The

Re: [Freesurfer] hippocampus subfields

Friday, 17 November 2017 at 12:41 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampus subfields Dear Eugenio, Thank you for your reply. I am sorry that I don't express it clearly. FIrstly, I ran egstats2label --subjects subjid --meas volume --segno 17 53 --t

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