Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

found in /Users/PageLab/Documents/freesurfer/bin The freesurfer environment has been set to /Users/PageLab/Documents/freesurfer So, I am not sure why the script is inaccessible. Recon-all works great. Thanks, Jasmin On Wed, Jul 11, 2018 at 9:08 AM, Iglesias Gonzalez, Eugenio

Re: [Freesurfer] /run_segmentSubjectT1_autoEstimateAlveusML.sh: Command not found.

External Email - Use Caution Dear Jasmin, The script segmentSF_T1.sh does not seem to be able to find basic commands like pwd and dirname. Are these in your path? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) Univer

Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

Jun27, 2018) Hippocampal subfield Matlab runtime Java error External Email - Use Caution Hi Eugenio, I’ve followed the wiki and installed it based on the instructions. My server runs on RHEL7. Best, Sean On Mon, Jul 2, 2018 at 3:47 PM Iglesias Gonzalez, Eugenio mailto:e.

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

: Iglesias Gonzalez, Eugenio Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: Anterior / Posterior Partition in Hippocampus parcellation atlas Dear Sir, I have another query if i use "export WRITE_POSTERIORS=1", will it generate posterior CA1 and other substructures in the for

Re: [Freesurfer] FS6.0-dev (Jun27, 2018) Hippocampal subfield Matlab runtime Java error

External Email - Use Caution That’s rather ugly. Sean: did you install the runtime from the Mathworks website, or did you download / uncompress following the instrucitons in the wiki? Andrew: any ideas? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

know. -- 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: Dev vasu Date: Monday, 2 July 2018 at 19:30 To: "Iglesias Gonzalez, Eugenio" Cc: &

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

subfield label numbers for CA1 head and CA1 body are not defined ,also can i assure CA1 body as posterior region and CA1 head as anterior ?. Thanks Vasudev On Mon, Jul 2, 2018 at 7:39 PM, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: Dear Vasudev, You can run the module

Re: [Freesurfer] Anterior / Posterior Partition in Hippocampus parcellation atlas

External Email - Use Caution Dear Vasudev, You can run the module described in that wiki page, and in the output file [lr]h.hippoAmygLabels-T1.v2x.mgz you will find segmentations for CA1 head, CA1 body, CA23 head, CA23 body, CA4 head, CA4 body, and hippocampal tail (note that we

Re: [Freesurfer] brainstem-structures different versions?

External Email - Use Caution Hi Niels, The atlas is the same, so you’ll get the same regions, but the actual segmentation code has improved since FS6.0 – therefore the 1.1 and 1.2 versions. The results should not be wildly different, though. Cheers, /Eugenio -- Juan Eugenio Igle

Re: [Freesurfer] Merging aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz

Mehul Sampat Date: Thursday, 21 June 2018 at 16:47 To: "Iglesias Gonzalez, Eugenio" Cc: Freesurfer Mailing List Subject: Re: Merging aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz Hi Eugenio, Thank you for your reply. The solution to blend the two segmentation will work for

Re: [Freesurfer] Merging aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz

://cmictig.cs.ucl.ac.uk/ From: Mehul Sampat Date: Thursday, 21 June 2018 at 04:10 To: Freesurfer Mailing List , "Iglesias Gonzalez, Eugenio" Subject: Merging aparc+aseg.mgz and brainstemSsLabels.v10.FSvoxelSpace.mgz Hi Eugenio and Bruce, We used freesurfer-6.0.0 to segment the brain-stem into different

Re: [Freesurfer] Error with Hippocampal Subfields and Amygdala Nuclei

External Email - Use Caution Hi Nick, I believe Doug had a similar problem (atlas not flipping for right hippocampus) because he mixed versions of FreeSurfer. Your call is definitely a bit weird… First, you’re running the hippocampal subfields with FS6. And then, you’re calling

Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?

agr...@gmail.com>@gmail.com<mailto:sallyagr...@gmail.com> (preferred) | sgrace<mailto:sgr...@swin.edu.au>@swin.edu.au<mailto:sgr...@swin.edu.au> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Wednesday, 6 June 2018 6:09:24 PM To: Freesur

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

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution Thanks, Nikita. Can you please send us the file long-hippocampal-subfields-T1.log, which you can find under the base subject, for one of the failing cases? Cheers, /E -- Juan Eugenio Ig

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

. Sincerely, Nikita On Jun 12, 2018, at 10:05, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution Hi Nikita, Could you please be a bit more specific about your problem? What issue are you exactly referring to? Also, can you please send us t

Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files

External Email - Use Caution Hi Nikita, Could you please be a bit more specific about your problem? What issue are you exactly referring to? Also, can you please send us the log file of the hippocampal subfields (rather than of recon-all)? Cheers, /Eugenio -- Juan Eugenio Iglesi

Re: [Freesurfer] Is amygdala nuclei segmentation possible in freesurfer version 5.3?

External Email - Use Caution Dear Sally, You will need to download the development version to access this functionality. However, if you have already run your subjects through recon-all with FS5.3, you can directly call segmentHA_T1.sh/ segmentHA_T2.sh/ segmentHA_T1_long.sh in th

Re: [Freesurfer] Problem in subfields development version (T2 mode)

/ From: "Iglesias Gonzalez, Eugenio" Date: Friday, 1 June 2018 at 00:30 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Problem in subfields development version (T2 mode) Dear all, The problem should be fixed in the Linux builds. The MAC update will come in the next couple

[Freesurfer] Problem in subfields development version (T2 mode)

External Email - Use Caution Dear all, The problem should be fixed in the Linux builds. The MAC update will come in the next couple of days. Apologies again for the inconvenience. /Eugenio Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) University College Lo

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

g the sources.sh) however, i have encountered another error (please find the attached hippocampal-subfileds-T1.log file). In this case, line 3 of kvlAutoCrop has a problem with kvlAutoCrop.bin Thanks, Best, Miracle On Wed, May 30, 2018 at 6:03 PM, Iglesias Gonzalez, Eugenio mailto:e.igles...@u

Re: [Freesurfer] creating a mask for the thalamus parcellations

External Email - Use Caution I probably shouldn’t say this, but I will, anyway: It’s coming soon! -- 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/ O

Re: [Freesurfer] midbrain mask in standard-space?

External Email - Use Caution Hi Dan, The mesh can be rasterized in its reference space, but such does not correspond to any volumetric image. Cheers, /Eugenio Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.co

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

e 43) with the command "source $FREESURFER_HOME/freesurfer/FreeSurferEnv.sh" and comment line 42? It might solve the problem. Best, Miracle On Wed, May 30, 2018 at 2:43 PM, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution

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

quot; I get " /opt/freesurfer-6.0.0". I always insert this lines " export FREESURFER_HOME=/opt/freesurfer-6.0.0/freesurfer; source $FREESURFER_HOME/SetUpFreeSurfer.sh" in all my bash scripts for freesurfer. Best, Miracle On Wed, May 30, 2018 at 12:47 PM, Iglesias

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

found this source $FREESURFER_HOME/sources.sh kvlAutoCrop.bin "$@" Can I edit the kvlAutoCrop file to point the correct? or something else Best, Miracle On Wed, May 30, 2018 at 11:55 AM, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Us

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

ssing because we installed the correct/recent matlab runtime. Best, Miracle On Wed, May 30, 2018 at 11:35 AM, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution Hi Miracle, I believe Doug (CCed) ran into a similar problem recently, and I think t

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

External Email - Use Caution Hi Miracle, I believe Doug (CCed) ran into a similar problem recently, and I think the problem had to do with mixing versions. What exact version are you using? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Im

Re: [Freesurfer] Subfields Development Version MATLAB:scriptNotAFunction

External Email - Use Caution Dear Lachian (and everyone), I am SO sorry about this. I’ll be fixed very soon, I promise. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.co

Re: [Freesurfer] Command to export hippocampal subfields segmentations

I obtained are mm with six decimals? For example, for the left_Hippocampal_tail I obtained 498.117062 Sorry for this absurd question but I would like be sure about this. Thanks in advance, Best 2018-05-29 16:50 GMT+02:00 Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>>:

Re: [Freesurfer] Command to export hippocampal subfields segmentations

command rmnlab1:~ neucoga$ quantifyHippocampalSubfields.sh T2_3D_SAG pruebahipocampo.txt /Applications/freesurfer/subjects Could be motivated this error due to read & write permissions on Mac folders? Thanks Best, 2018-05-29 10:54 GMT+02:00 Iglesias Gonzalez, Eug

Re: [Freesurfer] hippo subfields and amygdala

e the help Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 29 May 2018 11:44:41 To: Freesurfer support list Subject: Re: [Freesurfer] hippo subfields and amygdala External Email - Use Caution Hi

Re: [Freesurfer] hippo subfields and amygdala

External Email - Use Caution Hi Erik, The subfield module gives you a segmentation in the same space as brain.mgz and the rest of volumes in the recon-all stream: [lr]h.hippoAmygLabels-T1.v2x.FSvoxelSpace.mgz You can use mri_extract_label to create binary masks. Cheers, /Eugenio

Re: [Freesurfer] Command to export hippocampal subfields segmentations

the file anywhere. Thanks in advance 2018-05-29 10:34 GMT+02:00 Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>>: External Email - Use Caution Hola Miguel Ángel, What do you mean by exporting? The volumes? There is a command to gather the volumes from all subjects

Re: [Freesurfer] Command to export hippocampal subfields segmentations

External Email - Use Caution Hola Miguel Ángel, What do you mean by exporting? The volumes? There is a command to gather the volumes from all subjects in the subjects directory, which is: quantifyHippocampalSubfields.sh (in FreeSurfer 6.0) quantifyHAsubregions.sh (in dev version)

Re: [Freesurfer] T2 seq. for hippocampus ??

External Email - Use Caution I think it’s an empirical question. I would try both on a bunch of subjects and then decide. But my gut feeling is that T1+T2 will do best. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University Col

Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

/ From: "Hoopes, Andrew" Date: Tuesday, 8 May 2018 at 16:27 To: "Iglesias Gonzalez, Eugenio" , Freesurfer support list Subject: Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem I’m not sure. How long do these runs usually take Eugenio? I’m noticing th

Re: [Freesurfer] Longitudinal hippocampal subfields analysis problem

External Email - Use Caution Is it possible that it ran out of memory? Andrew, what do you think? -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

re not the named recipient(s), please notify the sender at the email address above, delete this email from your computer, and destroy any copies in any form immediately. From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, E

Re: [Freesurfer] T2 weighted images as input for recon-all command

(subfolder) Inside the subfolder orig i have two files T2.nii and T2.mgz (T2.mgz was previously generated using mir_convert command) Why don´t find the file? Thanks for your help Cheers, 2018-05-04 10:50 GMT+02:00 Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk

Re: [Freesurfer] T2 weighted images as input for recon-all command

d with ERRORS at Fri May 4 10:43:04 CEST 2018 Thanks cheers, 2018-05-04 10:00 GMT+02:00 Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>>: External Email - Use Caution Sorry if I didn’t explain myself properly. T2 scans of the whole head can be used by recon-all to

Re: [Freesurfer] T2 weighted images as input for recon-all command

t for recon-all command. Regards, Janani From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: 04 May 2018 12:50 To: Freesurfer support list ; Freesurfer support list Subject: Re: [Freesurfer] T2 weighted i

Re: [Freesurfer] T2 weighted images as input for recon-all command

External Email - Use Caution Hola Miguel Ángel, First, you need to run the T1 through recon-all normally, as you have already done. Next, you run the subfield module with the highres T2 as input - no recon-all on the T2 required, as it's used in a different way. Cheers Eugenio S

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

one > On May 3, 2018, at 3:47 AM, Iglesias Gonzalez, Eugenio > wrote: > > Eugenio ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intend

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

180’). If you could guide me on how to best re-register my DTI NIFTI images to the norm.mgz image, that would be great. Thanks, Mark From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Thursday, May 3, 2018 3

Re: [Freesurfer] kvlGEMSMatlab error: search direction is not a descent direction

External Email - Use Caution Dear Wayne, We have an idea of what the problem might be and will look into it soon. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs

Re: [Freesurfer] Extracting DTI/NODDI data from hippocampal subfields

External Email - Use Caution Dear Mark, Just to make sure we’re on the same page: I’ll say that two images are in the same voxel space when they have the same size (in voxels, e.g., 256x256x256) and the same vox2ras matrix - the one that maps voxel coordinates to RAS (physical)

Re: [Freesurfer] Hippocampal subfield analysis did not run or produce right hemisphere outpus

External Email - Use Caution Hi Zola, What version of FreeSurfer was this? Can you please send us the log? Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Zola Mannie

Re: [Freesurfer] question about hippocampal vols

, 2018 at 11:04 AM, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution Dear Ani, What was the exact command you used? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College Londo

Re: [Freesurfer] question about hippocampal vols

External Email - Use Caution Dear Ani, What was the exact command you used? 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/ From: on behalf of Anik

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

Re: [Freesurfer] using T2 for hippo subfields

you have received this email in error, please immediately notify the sender via telephone or return email.” From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, April 20, 2018 12:27 PM To: Freesurfer su

Re: [Freesurfer] using T2 for hippo subfields

arvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, April 20, 2018 9:23 AM To: Freesurfer support list Subject: Re: [Freesurfer] using T2 for hippo subfields External Email - Use Caution Of course! https://surfer.nmr.mgh.h

Re: [Freesurfer] using T2 for hippo subfields

limeter T1 datasets processed using FS6.0? If yes, where can I upload to? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, April 20, 2018 7:58 AM To: Freesurfer support list Subject: Re: [

Re: [Freesurfer] using T2 for hippo subfields

rom: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Thursday, April 19, 2018 1:57:18 PM To: Freesurfer support list Subject: Re: [Freesurfer] using T2 for hippo subfields External Email - Use Caution Hi Jim, >From my experience .8 isotropic is on t

Re: [Freesurfer] using T2 for hippo subfields

presume I can still use the -hippocampal-subfields-T1 option in the traditional recon-all -all stream? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Thursday, April 19, 2018 1:57:18 PM To: Freesurfer support li

Re: [Freesurfer] using T2 for hippo subfields

aces. > > Is an 'expert_file' required ?? > > > Jim > > __ > __________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Iglesias > Gonzalez, Eugenio > Sent: Friday, March 23, 2018 11:02:00 AM > To: Freesurfer s

Re: [Freesurfer] Lateral Geniculate Nucleus (LGN) roi or volume measures?

I probably shouldn’t say this too loud but, after many delays, I might be close to having a working atlas of the thalamic nuclei that I would like to release in FreeSurfer. Hopefully in a couple of months… -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University

Re: [Freesurfer] which dev version for amygdala segmentation

Hi Ani, sorry for the slow response (Easter...). The script should be in $FREESURFER_HOME/bin, which is automatically added to your path when you source FreeSurfer. Cheers, /Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http

Re: [Freesurfer] using T2 for hippo subfields

Hi Jim, In the end it’s an empirical question, but my gut feeling is that the T1 with hi-res flag will be best. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on b

Re: [Freesurfer] Hippocampal Subfields Module, output error

Thanks, Aura. What exact version of FreeSurfer are you using? I’m assuming it’s a development version, but from when? The results are indeed weird… -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.

Re: [Freesurfer] Hippocampal subfields

Dear Arsenije The atlas is encoded in a tetrahedral mesh, so there is no nifti file for it. Having said that, it is possible to rasterize the atlas at a target resolution. The command is the following: kvlRasterizeAtlasMesh $FREESURFER_HOME/average/HippoSF/atlas/AtlasMesh.gz $FREESURFER_HOME/ave

Re: [Freesurfer] Regarding hippocampus tesellation

Hi Pooja I'd suggest reading in the mgz volume with MATLAB (you can use the function MRIread in $FREESURFER_HOME/matlab) and export it to your favorite format from there Cheers Eugenio Sent from my phone, please excuse brevity and typos From: pooja prabhu Sent:

Re: [Freesurfer] Hippocampal Subfields Module, output error

Hi Aura, 1. What do you mean by “loading Matlab 8.2”? It should be Matlab 8.4 (2014b). 2. “Some still did”: what error did you get? - Also, I’m confused by what you wrote, that subfields worked but hippocampal module didn’t (aren’t they the same thing?) - Finally: can you please send us a screen

Re: [Freesurfer] Hippocampal Subfield Atlas

It’s in $FREESURFER_HOME/average/HippoSF/atlas But it’s not straightforward to visualize it… 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/ From: on behalf of Rober

Re: [Freesurfer] no file ‘volumesAmygdla.txt’ from FS6.0 - Jan. 2017 release

Yes! It's all fine. It was just a placeholder for the segmentation of the nuclei of the amygdala, which is available in there development version. Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on

Re: [Freesurfer] running -hippo-subfields with both T1 and T2 using FS 6.0

Looks good to me! Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: Tuesday, March 13, 2018 1:06:25 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] running -hi

Re: [Freesurfer] Invalid MEX file - FS dev-version error?

You’re missing your license file. https://surfer.nmr.mgh.harvard.edu/fswiki/License -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Reetta-Liina Armio Reply-To:

Re: [Freesurfer] Hippocampal Subfield Error

Hi Theo, Sorry for not being more clear; I meant hippocampal-subfields-T1.log, which should be in the directory “scripts”. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.a

Re: [Freesurfer] Hippocampal Subfield Error

Dear Theo, Would you mind sending up the log of the hippocampal subfields as well? 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/ From: on behalf of "AKUDJEDU, THE

Re: [Freesurfer] Hippocampal Subfield Error

Dear Theo, Can you please provide us with the command you executed, and the complete output logs? 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/ From: on behalf of

Re: [Freesurfer] segmentHA_T2.sh

We are looking into all this. We’ll have updates soon. 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/ From: on behalf of Eva Hilland Reply-To: Freesurfer support

Re: [Freesurfer] dev version

Dear Zheng, Question 1: In the dev version, all labels are rendered by default. In previous versions: it’s probably best to open the file twice, and render the hippo with the range 200-249 and the amygdala with the range 7000-7020. Question 2: open lh.hippoAmygLabels-T1.v2x.mgz instead of lh.h

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

I’ve never tried. Koen/Oula, what do you think? -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Gabor Perlaki Reply-To: Freesurfer support list Date: Tuesday, 2

Re: [Freesurfer] Hippocampal subfields segmentation

Hi Alexis, Yes please send me the images! Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Alexis Guyot Reply-To: Freesurfer support list Date: Monday

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

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

Hi Cassie, It seems to be a problem with mri_robust_register, when trying to allíen the t1 and t2 scans. Martin, any ideas? Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Cassandra Wannan Sent: Th

Re: [Freesurfer] Hippocampal Sub-field volume units

Short answer: yes, it’s cubic mm. -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of "Crawford, Anna" Reply-To: Freesurfer support list Date: Wednesday, 17 Januar

Re: [Freesurfer] Issues with hippo subfields / amygdala fixed

Good point, Arkadiy. Essentially, the binaries were expecting the Matlab 2014b runtime to be present, but the rest of scripts were still assuming Matlab 2012b (those are the files that were not committed). This should only have happened if you downloaded the dev version between December 23rd and

[Freesurfer] Issues with hippo subfields / amygdala fixed

Dear all, The problems with the hippocampal subfield / nuclei of amygdala module (as well as with the brainstem module) in the dev version should now be fixed. I apologize for the inconvenience these issues might have caused. I rushed to leave everything ready right before the winter break and ma

Re: [Freesurfer] Amygdala segmentation runtime error

Dear all, I’ve found out what the problem was; it was to do with the switching from Matlab R2012b runtime to R2014b. I’ll fix this as soon as possible and let you know. Apologies for all the inconvenience this might have caused. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow

Re: [Freesurfer] making masks with subfields etc

freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 12 January 2018 14:21 To: Freesurfer support list Subject: Re: [Freesurfer] making masks with subfields etc Dear Erik, I might be missing something here, but: the subfie

Re: [Freesurfer] making masks with subfields etc

Dear Erik, I might be missing something here, but: the subfield segmentation, rawavg.mgz, etc, are all already in native subject space… Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.

Re: [Freesurfer] Amygdala segmentation runtime error

Hi Emily, When did you download the dev version? Was it very recently? Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of Emily K Clarke Reply-To: Freesu

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

depend on this executable anymore -- Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 10/01/2018, 21:29, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gon

Re: [Freesurfer] Amydala segmentation

Dear Zheng, You need to download the whole dev version, not just the script ;-) Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research 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.co

Re: [Freesurfer] hippocampal subfields in younger populations

Dear Christian, They atlas is built using subfield segmentations on scans of older adult brains, but: 1. it’s also built with whole hippocampus segmentations of scans of subjects of a wider age range. 2. the deformation model should be able to account for large parts of the anatomical differenc

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-boun..

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 b

Re: [Freesurfer] Hippocampus subfield ROI

Hi JK, You can use mri_extract_label: https://surfer.nmr.mgh.harvard.edu/fswiki/mri_extract_label 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/ From: on behalf of

Re: [Freesurfer] Hippocampal Subfield and Amyg Nuclei ICV Correction

Hi Arkadiy 1. Yes 2. If you’re correcting the subfields by hippocampal volume: a) the question is a different one (“which fraction of the hippo volume is attributed to each subfield”); and b) I wouldn’t correct by ICV, because the values are already fractions / normalized (see point a). Cheers,

Re: [Freesurfer] freesurfer version update issue in MacOS

The answer is yes, indeed. Just be careful when you report your results, specifying which version you used for what. 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/

Re: [Freesurfer] new Amygdala and Hippocampus segmentation

your help. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: 08 December 2017 14:29 To: Freesurfer support list Subject: Re: [Freesurfer] new Am

Re: [Freesurfer] new Amygdala and Hippocampus segmentation

Hi Erik, You can runsegmentHA_T2.sh on your FS processed subjects. You don’t need to run segmentHA_T1.sh first. The choice is whether you want to use T1+FLAIR (USE_T1=1) or only FLAIR (USE_T1=0). This command will generate outputs for both hippocampus and amygdala. The output will include multi

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Hi again, You can find the detailed protocols here: http://adni.loni.usc.edu/methods/documents/mri-protocols/ Click on your scanner model (or similar) and search for the sequence “HighResHippcampus”. Regarding the distortion correction: I’ll leave this one for Andre ;-) Cheers, /Eugenio -- Juan E

Re: [Freesurfer] MRI protocol for hippocampal subfield segmentation

Hi Gabor, A good place to start is ADNI’s high-res hippocampal T2 protocol. You can find the details on their website. It’s a coronal, anisotropic acquisition of a slab covering the hippocampus (0.4mm in plane, 2mm thickness, 25-30 slices). I’ve been playing a bit with more isotropic acquisition

Re: [Freesurfer]  hippocampus subfields

Dear Zheng, You can build a GLM with a single group, and then look at the residuals. Or, even easier: just divide the volumes of each subject by his/her ICV (the answers won’t be identical, but should definitely be quite similar). Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fe

[Freesurfer] Postdoctoral position in Machine Learning for 3D Histology

Dear all, We are looking for a postdoc to work on my ERC Starting Grant project "Building Next-Generation Computational Tools for High Resolution Neuroimaging Studies", at the Translational Imaging Group (TIG) at University College London (UCL)

Re: [Freesurfer] error in segmentHA_T2.sh

Hi Cong, This totally looks like a problem with absolute/relative paths. Can you please try again, but using the full path to the T2? Something like: segmentHA_T2.sh control004 /Users/cong/data/subjects/control004/mri/T2.nii T2 1 If this works, let me know and I’ll fix the code. Cheers, /E --

Re: [Freesurfer] hippocampal subfields stats

Dear Donatas, I believe that mri_segstats is just counting voxels using the hard segmentation, whereas the volume in lh.hippoSfVolumes-T1.long.v20.txt is obtained using a soft segmentation. If you’re interested in this, look up the WRITE_POSTERIORS option in the wiki. Cheers, /Eugenio -- Juan

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