Re: [Freesurfer] Hippocampal subfields

To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields Oh, now I understand. Yeah you can add the head, body and tail segments of each subfield to get 6.0 type of measurements ;-) Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL

Re: [Freesurfer] Hippocampal subfields

day 27 August 2021 22:02 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Hippocampal subfields Dear Erik I’m not sure I understand. What does your output file look like? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (

Re: [Freesurfer] Hippocampal subfields

...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Juan E. Sent: Friday 27 August 2021 22:02 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields Dear Erik I’m not sure I understand. What does your output file look like? Cheers, /Eugenio Juan Eugenio Iglesias Senior

Re: [Freesurfer] Hippocampal subfields

Dear Erik I’m not sure I understand. What does your output file look like? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com On Aug 27, 2021, at 16:14, Erik O'Hanlon mailto:ohanl...@tcd.ie>> wrote: External

Re: [Freesurfer] Hippocampal Subfields/ASEG

External Email - Use Caution Hi Philipp, Thank you very much! This was very helpful! Best, Yiota On Mon, Jun 21, 2021 at 3:38 PM Saemann, Philipp wrote: > External Email - Use Caution > > Hello Yiota, > > > the whole hippocampus value is a sum of all subregions

Re: [Freesurfer] Hippocampal Subfields/ASEG

External Email - Use Caution Hello Yiota, the whole hippocampus value is a sum of all subregions except for the hippocampal fissure - best try to reproduce this in an example. The recon-all pipeline also delivers a total hippocampal volume, but it is an entity/result of its

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

e and run a step directly (both with "" > empty value and the values below) ..." Hope to that helps! Regards, Chester -- Message: 4 Date: Fri, 11 Jun 2021 11:43:21 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Hippoca

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

ct line so it is more specific >> than "Re: Contents of Freesurfer digest..." >> >> >> Today's Topics: >> >> 1. Re: Hippocampal Subfields error "no such file or >> directory"/"dyld library not loaded" (Iglesias Gonzalez, Juan E.) >> 2. Ill-Con

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

z, Juan E.) > 2. Ill-Conditioned/Badly Scaled Matrix Error (Lurie, Lucy) > 3. LGI FS 7.1 (Del Re, Elisabetta) > 4. mri_glmfit with pvr (std...@virgilio.it) > 5. Re: FW: WM or Pial edits to correct surfaces (Fischl, Bruce) > > >---------

Re: [Freesurfer] Hippocampal Subfields error "no such file or directory"/"dyld library not loaded"

Dear Chester, What command did you exactly run? There seems to be a mix of T1 and T1+additionalMRI segmentation commands in there. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com > On Jun 9, 2021, at 00:23, Chester

Re: [Freesurfer] Hippocampal Subfields

: Re: Hippocampal Subfields Okay, Thank you very much Philipp. Best, Saurabh From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Saemann, Philipp Sent: Thursday, April 22, 2021 2:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer

Re: [Freesurfer] Hippocampal Subfields

: [Freesurfer] Hippocampal Subfields * External Email - Caution * External Email - Use Caution Hi Saurabh, you have to run (and QC) recon-all before, Best, Philipp Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Jindal, Saurabh

Re: [Freesurfer] Hippocampal Subfields

External Email - Use Caution Hi Saurabh, you have to run (and QC) recon-all before, Best, Philipp Von: freesurfer-boun...@nmr.mgh.harvard.edu im Auftrag von Jindal, Saurabh Gesendet: Donnerstag, 22. April 2021 20:55 An:

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

To: fsbuild , freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error External Email - Use Caution External Email - Use Caution Hi 'E' / 'R', I even tried changing the resolution to 1.0 with no success ruling put memory issues

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

Thank you both! On Linux, 8GB is insufficient, and 16GB is normally sufficient; I wonder if the requirements are a bit higher on MAC? Could you please try the following? 1. Edit $FREESURFER_HOME/bin/segmentHA_T1.sh (might require sudo) 2. Replace the line: set

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

: Ramtilak Gattu Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error Maybe you could let us know if the system integrity protection feature is turned on the Mac (which is the default). The following command will report if it is enabled or disabled, e.g., when enabled

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

External Email - Use Caution Maybe you could let us know if the system integrity protection feature is turned on the Mac (which is the default). The following command will report if it is enabled or disabled, e.g., when enabled, $ csrutil status System Integrity Protection

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

59 EDT 2021 For more details, see the log file /Users/tilak/Desktop/Work/CNS_cases/Hipps/Amy_Damboise/scripts/hippocampal-subfields-T1.log tilak@tilak Hipps % From: fsbuild Sent: Tuesday, March 23, 2021 11:00 PM To: freesurfer@nmr.mgh.harvard.edu Cc: Ramti

Re: [Freesurfer] Hippocampal Subfields Segmentation Violation-error

External Email - Use Caution I”m wondering if this is an issue with the version of Java installed on the machine and Matlab. I’ve seen the latest MCR Matlab installer try to make changes to java installed on a Mac. So maybe updating or re-installing the Matlab software on your

Re: [Freesurfer] Hippocampal subfields questions

Hi Steve, Thank you very much for the interest in our tool! Q1. Yes, mm^3. Q2. I’ll defer to Doug Greve (CCed)  Cheers, /E Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Steve Petersen Reply-To: Freesurfer

Re: [Freesurfer] Hippocampal subfields error

dataset we need to be able to extract the older hippocampal subfields, starting with the recon-all hippocampal subfields processing. Thanks, Emily Date: Wed, 9 Sep 2020 21:21:41 + From: "Iglesias Gonzalez, Juan E." Subject: Re: [Freesurfer] Hippocampal subfi

Re: [Freesurfer] hippocampal subfields error

External Email - Use Caution The whole log message: # #@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT 2020 -- Setting up environment variables --- LD_LIBRARY_PATH is

Re: [Freesurfer] hippocampal subfields error

Dear Courtney, You can safely ignore “This file does not contain MRI parameters”. If the output files are not created, there must be another error further down. Could you please send us the whole output? Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and

Re: [Freesurfer] Hippocampal subfields --> normalization

Dear Hae Won, Normalizing by ICV and whole hippocampal volume simply attempt to answer two different questions: Is the volume of subfield X, accounting for head size, [insert analysis question here]? Is the % of hippocampal volume covered by subfield X, [insert analysis question here]? (where

Re: [Freesurfer] Hippocampal subfields

Dear Ioana, This is tricky because the volumes are computed from soft segmentations, which are not the ones you’re editing. In general, editing outputs is a bad idea; it may be better to simply discard the cases for which quality control fails. Having said that: if you want to use corrected

Re: [Freesurfer] hippocampal-subfields-T1 error

:07 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal-subfields-T1 error This email from jiglesiasgonza...@mgh.harvard.edu originates from outside Imperial. Do not click on links and attachments unless you recognise the sender. If you trust the sender, add them to your safe

Re: [Freesurfer] hippocampal-subfields-T1 error

Dear Aleks, Please try: chmod u+x /rds/general/project/amyloidpet/live/freesurfer/bin/* Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Duvnjak, Aleksandar" Reply-To: Freesurfer support list

Re: [Freesurfer] hippocampal-subfields-T1 error

External Email - Use Caution To clarify, upon copying the entire FreeSurfer 6.0 package to our personal directory, we have then downloaded the matlab runtime MCRv80 folder to that directory and the issue does not appear to be the hippocampal-subfields-T1 pipeline accessing

Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version External Email - Use Caution Dear Juan, Thank you very much for you answer! However, I ran into another issue using the new tool: It

Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

External Email - Use Caution Dear Juan, Thank you very much for you answer! However, I ran into another issue using the new tool: It is stated:  'Using the additional scan in isolation is advised when it is of higher resolution than the T1 while covering the whole hippocampi

Re: [Freesurfer] Hippocampal subfields FS6 vs. new hippocampus tool (incl Amygdala) FreeSurfer_dev version

Hi Rene, The atlases are slightly different so the outputs will be a bit different. But the segmentations will indeed be comparable. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Rene Seiger

Re: [Freesurfer] Hippocampal subfields: exporting results

fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Steve Petersen Reply-To: Freesurfer support list Date: Wednesday, 11 December 2019 at 10:28 To: "freesurfer@nmr.mgh.harvard.edu" Subject: Re: [Freesurfer] Hippocampal subfields: exporti

Re: [Freesurfer] Hippocampal subfields: exporting results

External Email - Use Caution Dear Eugenio, I noticed what was the problem. I used freesurfer dev version with the following command: segmentHA_T2.sh I tried to export the hippocampal and amygdala results of several subjects with these commands and now everything works fine.

Re: [Freesurfer] Hippocampal subfields: exporting results

Dear Steve, Can you please send us: - The segmentation command you used for a sample subject - A list of the files under the mri directory for that subject. Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on

Re: [Freesurfer] hippocampal subfields as masks for mri_segstats

Try using this instead lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz On 12/4/19 5:09 PM, Marcel Heers wrote: > > External Email - Use Caution > > Dear all, (dear Eugenio), > > I would like to use hippocampal subfields as masks for mri_segstats to > retrieve intensity values. I am having

Re: [Freesurfer] hippocampal subfields as masks for mri_segstats

I believe the problem is that they live in different voxel spaces (Doug, can you please clarify?) Cheers, /Eugenio Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Marcel Heers Reply-To: Freesurfer support list

Re: [Freesurfer] Hippocampal Subfields Atlas

Are you using fsfast? On 9/25/19 7:00 AM, ZZY wrote: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > Dear ?0?2Doug?? > > ?0?2 ?0?2 ?0?2I have a group of multimode MRI data, including functional MRI, > T1WI and diffusion MRI. We want to analyze the functional and > structual

Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

glad it worked out Bruce On Fri, 13 Sep 2019, 3 6 wrote: External Email - Use Caution Hi Bruce, I checked the alias, I really aliased mv to “mv -i”, and it worked automatically, after I unaliased. Thanks for your help. Best regards, Guodong 在

Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

External Email - Use Caution Hi Bruce, I checked the alias, I really aliased mv to “mv -i”, and it worked automatically, after I unaliased. Thanks for your help. Best regards, Guodong > 在 2019年9月13日，上午12:00，freesurfer-requ...@nmr.mgh.harvard.edu 写道： > > Re:

Re: [Freesurfer] Hippocampal-subfields-T1 interruption

Hi Guodong Hmmm, not sure what is doing that, but my guess is you have mv aliased. Can you type: which mv and see if you have it aliased to "mv -i" or some such? cheers Bruce On Thu, 12 Sep 2019, 3 6 wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm

Re: [Freesurfer] Hippocampal subfields

support list Date: Friday, 9 August 2019 at 01:19 To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields External Email - Use Caution Dear /Eugenio, Here is the log files and all results for one subject as the attachments. I have run a lots of subjects and all result

Re: [Freesurfer] Hippocampal subfields

External Email - Use Caution Dear /Eugenio, Here is the log files and all results for one subject as the attachments. I have run a lots of subjects and all result directories didn't include l(r)h.hippoSfLabels-T1.v10.mgz file. Sincerely, Zheng At 2019-08-08 09:49:30,

Re: [Freesurfer] Hippocampal subfields

Dear Zheng, Can you please send us the log files? Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of 郑凤莲 Reply-To: Freesurfer support list Date: Wednesday, 7 August 2019 at 21:19 To:

Re: [Freesurfer] hippocampal subfields error

pport list Date: Monday, 17 June 2019 at 10:11 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields error   External Email - Use Caution Dear Eugenio,   attached you’ll find the picture. Looks as though the left hippocampus has erroneously been attribut

Re: [Freesurfer] hippocampal subfields error

) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Mennecke, Angelika" Reply-To: Freesurfer support list Date: Monday, 17 June 2019 at 10:11 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields error External Email - Use Caution De

Re: [Freesurfer] hippocampal subfields error

External Email - Use Caution Dear Angelika, Can you please send us a screenshot of the inaccurate T1 segmentation? Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of "Mennecke,

Re: [Freesurfer] Hippocampal subfields segmentation template

External Email - Use Caution Dear Wu, The “templates” are probabilistic atlases with no image intensities. All you can look at is images like the ones in the top panel of Figure 5 in the paper. If you want to generate these, let me know and I’ll show you instructions (it’s a bit

Re: [Freesurfer] hippocampal subfields

External Email - Use Caution Thanks, Marcel. Can you please send us the whole output (can be found in the log file) Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com

Re: [Freesurfer] hippocampal subfields error

External Email - Use Caution That sounds pretty weird… Did you get any error messages on the Linux server? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com

Re: [Freesurfer] hippocampal subfields segmentation error

tp://www.jeiglesias.com > > http://cmictig.cs.ucl.ac.uk/ > > > > > > *From: * on behalf of 오진영 < > jinyoung.oh...@gmail.com> > *Reply-To: *Freesurfer support list > *Date: *Monday, 30 July 2018 at 09:29 > *To: *Freesurfer support list > *Subject

Re: [Freesurfer] hippocampal subfields segmentation error

-To: Freesurfer support list Date: Monday, 30 July 2018 at 09:29 To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields segmentation error External Email - Use Caution Dear Eugenio, Thanks for your reply. I am running version "freesurfer-Darwin-OSX-stable-pub-v6.0.0-2b

Re: [Freesurfer] hippocampal subfields segmentation error

External Email - Use Caution Dear Jinyoung, Can you please send us the log, or at least the last few lines before the error? Also, which exact version are you using? 6.0 or dev? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image

Re: [Freesurfer] Hippocampal Subfields Module, output error

t <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Friday, 23 March 2018 at 05:28 To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Hippocampal Subfields Module, output er

Re: [Freesurfer] Hippocampal Subfields Module, output error

er@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Hippocampal Subfields Module, output error Hi Eugenio, Thank you for replying so quickly to my lengthy message. I correct some of my statements, 1. Matlab 8.4 was used (not 8.2) 2. When I ran the cross-sectional subfield command, I

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

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

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

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

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

Re: [Freesurfer] hippocampal subfields downsampling question

Great question! El 26/10/2017 17:09, "NIELS JANSSEN ." escribió: > In the mri output folder, I noticed that both the 0.33 mm and 1 mm > (voxelspace) maps have subfields that do not overlap in space, meaning that > each subfield occupies a unique location in space that does

Re: [Freesurfer] hippocampal subfields downsampling question

Hi Niels, The code works at .33 mm and ends up with a soft segmentation for each voxel, i.e., each voxel has a vector of probabilities corresponding to the different structures. So, they DO overlap. However, we don’t write those probabilities by default. Instead, we take the most likely label

Re: [Freesurfer] hippocampal subfields: which are previous step result (files) needed for the process?

Hi Guido, I think you should wait until recon-all is done. Running 2 recon-all commands on the same subject simultaneously: a) would need hacking recon-all; b) it’s a bad idea. Moreover, the subfields make use of wmparc.mgz, which is produced towards the very end of recon-all -all anyway.

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

017 11:34 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability Hi again, Prad, In that case, you don’t need the discrete segmentations. Just look at the posteriors directly. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational I

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

ac.uk<mailto:e.igles...@ucl.ac.uk>> Sent: Wednesday, March 22, 2017 11:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability Hi Prad, The final probabilities are in the posterior files. There’s no need to binarize ?h.hippoSfLabels if what you’

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

edu> on behalf of Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk> Sent: Wednesday, March 22, 2017 11:06 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability Hi Prad, The final probabilities are in the posterior files. There’s no need

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

mgh.harvard.edu> <freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> Sent: Tuesday, March 21, 2017 2:22 PM To: Freesurfer support list Subject: Re: [F

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk> Sent: Tuesday, March 21, 2017 2:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfields Posterior Probability Dear Prad, There

Re: [Freesurfer] Hippocampal Subfields Posterior Probability

Dear Prad, There is a “secret” way of getting the posteriors. You need to set the environment variable WRITE_POSTERIORS to 1 before you call recon-all. In (t)csh: setenv WRITE_POSTERIORS 1 In bash: export WRITE_POSTERIORS=1 And then call recon-all -hippocampal-subfields-T1(T2) as usual. The

Re: [Freesurfer] hippocampal subfields - T1

: Re: [Freesurfer] hippocampal subfields - T1 Hi Batool, It’s not ideal, but if FreeSurfer does a decent job with the recon, something decent should come out of the subfields. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London

Re: [Freesurfer] hippocampal subfields - T1

Hi Batool, It’s not ideal, but if FreeSurfer does a decent job with the recon, something decent should come out of the subfields. Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com

Re: [Freesurfer] hippocampal subfields in average space

Hi Lauri, it depends on what you mean by template. If you mean an intensity averaged image, then no. But if you mean probabilities in a reference space, then yes. You can visualize the atlas with (warning: the viewer is a big buggy): cd $FREESURFER_HOME/average/HippoSF/atlas

Re: [Freesurfer] hippocampal subfields analysis command

mgh.harvard.edu> [freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>] Sent: Monday, February 13, 2017 11:49 AM To: Freesurfer support list Subject: Re: [Fre

Re: [Freesurfer] hippocampal subfields analysis command

mr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>] Sent: Monday, February 13, 2017 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields analysis command H

Re: [Freesurfer] hippocampal subfields analysis command

...@nmr.mgh.harvard.edu] on behalf of Iglesias Gonzalez, Eugenio [e.igles...@ucl.ac.uk] Sent: Monday, February 13, 2017 11:49 AM To: Freesurfer support list Subject: Re: [Freesurfer] hippocampal subfields analysis command Hi Batool What are the contents of hippo.txt? Just empty? Cheers, /Eugenio Juan Eugenio

Re: [Freesurfer] hippocampal subfields analysis command

Hi Batool What are the contents of hippo.txt? Just empty? 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 13 Feb 2017, at 16:41, Rizvi, Batool

Re: [Freesurfer] Hippocampal Subfields Segmentation Error

<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> namens Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> Verzonden: woensdag 25 januari 2017 12:30 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer]

Re: [Freesurfer] Hippocampal Subfields Segmentation Error

arvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> namens Iglesias Gonzalez, Eugenio <e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>> Verzonden: woensdag 25 januari 2017 12:30 Aan: Freesurfer support list Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error Dear M

Re: [Freesurfer] Hippocampal Subfields Segmentation Error

list Onderwerp: Re: [Freesurfer] Hippocampal Subfields Segmentation Error Dear Michel, What exact platform are you using? Ubuntu 14.04 installed on a virtual machine running on Windows 10? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University C

Re: [Freesurfer] Hippocampal Subfields Segmentation Error

Dear Michel, What exact platform are you using? Ubuntu 14.04 installed on a virtual machine running on Windows 10? 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

Re: [Freesurfer] hippocampal subfields

Dear Ferdi, It is really hard for us to know why you‘re getting such a weird error (segfault of kvlAutoCrop) in a submitted job when you don’t get it in an interactive session … You will have to look into the peculiarities of the submission system to see what is changing from one setting to the

Re: [Freesurfer] Hippocampal subfields total volume differences

Wow, longitudinal segmentation is absolutely awesome! It reduced our measurement error by more than 30%. I can't wait when the hippocampal longitudinal segmentation is ready. By the way, I want to run (cross-sectional) hippocampal subfields on longitudinal data using additional T2 with lower

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

ok thanks a lot for the quick answer. let me know when it works. our mri voxel size is 1 mm isotropic. (if it changes anything, I am working on ubuntu 14.04). Cheers, Pierre On Wed, Jul 20, 2016 at 11:15 AM, Iglesias, Eugenio wrote: > Thanks a lot, Pierre. > I’ll get

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

Thanks a lot, Pierre. I’ll get this sorted out as soon as possible. I’m in the process of modifying the module so it supports data with resolution >1mm, and also incorporating the longitudinal segmentation method described in https://doi.org/10.1016/j.neuroimage.2016.07.020 Cheers, Eugenio

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

Hi, I downloaded the new freesurfer development version and I still have the same problem when running the hippocampal-subfields "Invalid MEX-file '/tmp/MCR_4195017647/.mcrCache8.0/segmen0/autofs/cluster/koen/koen/GEMS-Release/bin/kvlGEMSMatlab.mexa64': libkvlGEMSCommon.so: cannot open shared

Re: [Freesurfer] Hippocampal subfields total volume differences

Dear Mojmir, using ~400 subjects, we found that the subfield module was a bit better than the ASEG volumes at discriminating Alzheimer’s patients from controls (see the Neuorimage paper). But, in any case, the difference is small. Regarding longitudinal segmentation: we just got a paper about

Re: [Freesurfer] Hippocampal subfields total volume differences

Hi Juan, Thanks! You're right, they really are tightly correlated (although their absolute values differ by 30%). We tried it on couple of subjects, but didn't find subfields to be significantly better than aseg stats though. By the way, is Freesurfer capable of using multiple scans from the same

Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?

The MAC version is now fixed as well. It should be available for download in the next couple of days (Zeke can provide a better estimate). Thanks again to all of you for your feedback. /E Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com

Re: [Freesurfer] Hippocampal subfields --> Can\'t find a *ctf file?

Dear Fernando, Are you using the MAC version? I haven’t finished fixing the bugs in that one yet. If you’re using the Linux version: Zeke, can you please shed some light on what the problem might be? Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London

Re: [Freesurfer] Hippocampal subfields total volume differences

Hi Mojmir, ASEG typically gives a larger estimate of the volume, though highly correlated with that from the subfield package. We have found the measurements from the subfield package to be a bit more reliable, though. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

And thanks to Zeke, of course ;-) Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 13 Jul 2016, at 11:19, Iglesias, Eugenio > wrote: Dear all, our expert

Re: [Freesurfer] Hippocampal subfields --> Can't find a *ctf file?

Dear all, our expert developer Zeke Kaufman figured out what the problem was. We have now fixed the Linux version; the MAC version will hopefully be ready as well in a couple of days. I have also fixed other bugs (including the problem that caused the code to get stuck every once in a while).

Re: [Freesurfer] hippocampal subfields command

ct: Re: [Freesurfer] hippocampal subfields command Hi Jim, the latter command uses a new, higher resolution atlas based on ex vivo scans. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Jul 2016, at

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

[freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>] on behalf of Iglesias, Eugenio [e.igles...@ucl.ac.uk<mailto:e.igles...@ucl.ac.uk>] Sent: Friday, June 10, 2016 3:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields segmenta

Re: [Freesurfer] hippocampal subfields command

Hi Jim, the latter command uses a new, higher resolution atlas based on ex vivo scans. Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 6 Jul 2016, at 15:39, Alexopoulos, Dimitrios

Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input?

, Eugenio [e.igles...@ucl.ac.uk] Sent: Friday, June 10, 2016 3:36 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfields segmentation - what is the voxel size of the input? Hi Matt, Bruce actually mentioned this possibility yesterday. Good to hear it doesn’t crash when you run

Re: [Freesurfer] Hippocampal Subfields Segmentation

: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of pierre deman <deman.pie...@gmail.com> Sent: Tuesday, July 5, 2016 7:04:21 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal Subfields Segmentation Hi, I still have a pro

Re: [Freesurfer] Hippocampal Subfields Segmentation

Hi, I still have a problem as well with the subfields segmentation (ubuntu 14.04, with the files .ctf) Cheers, Pierre Hello FreeSurfer Experts, I’m having issues with the hippocampal subfields segmentation using OS X Yosemite v10.10.5, Freesurfer dev version 6.0, Freesurfer Subject Stamp:

Re: [Freesurfer] Hippocampal Subfields Segmentation

I could finally look into this. It is indeed weird. The CTF is indeed embedded in the executable… Zeke/Nick, can you shed some light on this? Cheers, Eugenio Juan Eugenio Iglesias Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On 27

Re: [Freesurfer] Hippocampal Subfields Segmentation

Hi Pierre, Due to some technical problems, it might take me a couple of days to figure out what’s going on. But it definitely sounds funny that it is asking for the CTF, since this is supposed to be embedded in the executable… I’ll get back to you as soon as possible. Cheers, Eugenio Juan

Re: [Freesurfer] Hippocampal Subfields Segmentation

I tried that. but didn't work. Cheers, Pierre On Mon, Jun 27, 2016 at 4:32 PM, Iglesias, Eugenio wrote: > Hi everyone, > you need to install the Matlab 2012b runtime as explained in the wiki: > https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime > Cheers, > Eugenio >

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