Re: [Freesurfer] segmentHA_T2.sh longitudinal version?

External Email - Use Caution Dear Daniel, Such a script doesn’t exist yet (it’s in the to-do list). The reason why it’s not a straightforward extension of segmentHA_T1.sh is that resampling the anisotropic T2s to a common space is not a good idea, given the differences in

Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found {Disarmed}

nce. Best, CC From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Iglesias Gonzalez, Eugenio Sent: Friday, July 26, 2019 11:10 AM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not

Re: [Freesurfer] Hippocampal and Amygdala Segmentation Error - Command not found

External Email - Use Caution Dear CC, You need the development version of FreeSurfer, since the amygdala was added to the atlas after the 6.0 release. Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT)

Re: [Freesurfer] Pixel values in Brainstem segmentation {Disarmed}

from brainstemSsLabels.v10.mgz, I need the real pixel size of it, than I can calculate the real area size. Many Thanks! Best Jackie On Tue, Jul 16, 2019 at 11:16 AM Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution Dear Jackie, You may want

Re: [Freesurfer] Pixel values in Brainstem segmentation

External Email - Use Caution Dear Jackie, You may want to use the soft segmentations; you can obtain them by setting the environment variable WRITE_POSTERIORS to 1 before running the code, see: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Also: you can obtain

Re: [Freesurfer] Doubts in hippocampal subfields labeling {Disarmed}

External Email - Use Caution Thanks, Antonin. The ASEG has definitely oversegmented the hippo. Those large regions were ASEG and the subfield module disagree are mostly partial voluming of the lateral ventricle and the cerebral white matter or the fimbria, and are thus NOT

Re: [Freesurfer] Doubts in hippocampal subfields labeling

External Email - Use Caution Dear Antonin, It is difficult to see what’s going on in the images you sent. Would you mind uploading the subject, or at least sending us the image without the segmentation overlaid (and ideally, a sagittal view as well)? Cheers, /Eugenio -- Juan

Re: [Freesurfer] T2 seq. for hippocampus ?? {Disarmed}

External Email - Use Caution 1x1x3 is a no-no. The 1x1x1 FLAIR may or may not help; it’s hard to tell (especially without seeing the images!). But I would try both T1 and T1+FLAIR, and see what happens ;-) -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and

Re: [Freesurfer] Reposting a Question RE: Hippocampal/Amygdala subfield segmentation - Anterior Amygdala Area / Medial Nucleus Errors

External Email - Use Caution Dear David, These are all great questions. ASEG covers more voxels: the segmentations from the HA module are leaner than their ASEG counterparts (the volumes are very highly correlated, though). This is because the HA module operates at higher

Re: [Freesurfer] I have a question for "Segmentation of thalamic nuclei."

External Email - Use Caution Dear Gwang-Won, What version are you using? What’s the output of “recon-all –version”? Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Gwang-Won

Re: [Freesurfer] hippocampal subfields error

ar Eugenio, attached you’ll find the picture. Looks as though the left hippocampus has erroneously been attributed to gray matter. Cheers, Angelika Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Iglesias Gonzalez, Eugenio Gesendet: Montag

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] Segmentation of hippocampal subfields and nuclei of the amygdala

External Email - Use Caution Yes! The changes will probably be tiny, though. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Boris Rauchmann Reply-To: Freesurfer support list

Re: [Freesurfer] longitudinal subfields exited with ERRORS

External Email - Use Caution Dear Jaime, This is indeed a funny error. The left side runs to completion, and then the right side dies right away… Is the problem reproducible? Does it happen with other subjects, too? Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research

Re: [Freesurfer] brainstem - partial volume effects

External Email - Use Caution Hi Dusan, Volumes are computed from soft segmentations, which ameliorates the problems with partial voluming with the surrounding CSF. Kind regards, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT)

Re: [Freesurfer] Thalamus segmentation {Disarmed}

External Email - Use Caution Dear Zheng, The reticular nucleus is in the atlas and we use it to fit it to the image, but its segmentation is not always reliable and that’s why we don’t provide it (nor its volume). Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow

[Freesurfer] Postdoc position available

External Email - Use Caution Dear all, We are looking for a postdoc in our ERC project, with two main purposes. First, to improve the 3D histology reconstruction tools that we have been developing to build an ultra-high resolution atlas of the brain using histology. And

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] Thalamic segmentation

External Email - Use Caution Dear Zheng One of the other developers can help you with Freeview. But, as a workaround, you can always use an earlier version of Freeview, and load the lookup table of the Dev version. Cheers Eugenio Sent from mobile, please excuse brevity and typos

Re: [Freesurfer] Hippocampal subfield version

_ 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: Thursday, April 04, 2019 5:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Hippocampal subfield version External E

Re: [Freesurfer] Hippocampal subfield version

External Email - Use Caution Hi Emily, You need to download the dev version, but run the subfield/amygdala volume on cases reconned with FS6.0. Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

Re: [Freesurfer] segmentHA_T1.sh

External Email - Use Caution How about quantifyHAsubregions.sh? Cheers, /E -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on behalf of Daniel Callow Reply-To: Freesurfer support list Date: Monday, 1

Re: [Freesurfer] segmentHA_T1_long.sh HBT issue

External Email - Use Caution Dear Daniel, This is weird. Can you please send us lh.hippoAmygLabels-T1.long.v21.*.mgz for a sample subject? Cheers, /Eugenio -- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com From: on

Re: [Freesurfer] Conversion of thalamic nuclei labels {Disarmed}

Laboratory (CSAIL) Massachusetts Institute of Technology Lecturer on Radiology Harvard Medical School http://www.jeiglesias.com From: Valentina Mancini Date: Wednesday, 27 March 2019 at 10:08 To: "Iglesias Gonzalez, Eugenio" , Freesurfer support list Subject: Re: [Freesurfer]

Re: [Freesurfer] Conversion of thalamic nuclei labels

nt from mobile, please excuse brevity and typos > > > From: Valentina Mancini > Sent: Wednesday, March 27, 2019 5:56:34 AM > To: freesurfer@nmr.mgh.harvard.ed

Re: [Freesurfer] Conversion of thalamic nuclei labels

: Wednesday, March 27, 2019 5:56:34 AM To: freesurfer@nmr.mgh.harvard.edu Cc: Iglesias Gonzalez, Eugenio Subject: Conversion of thalamic nuclei labels Dear all, I ran the thalamic segmentation implemented in FreeSurfer and, according to visual inspection, I got nice results with a good delineation

Re: [Freesurfer] Thalamic nuclei segmentation

External Email - Use Caution Dear Zheng, Did the segmentation run to completion? Can you please send us the output? Cheers Eugenio Sent from mobile, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 郑凤莲

Re: [Freesurfer] segmentHA_T1_long.sh error {Disarmed}

External Email - Use Caution Hi Daniel, Can you please give us some more information? How did you call the script? Did you get any other output? Did the running case complete without errors? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical

Re: [Freesurfer] Thalamic nuclei longitudinal analysis

External Email - Use Caution Dear Antti, There’s no specific longitudinal version of the thalamic nuclei yet (hopefully one day…) You could naively segment the subjects in a cross-sectional fashion, but I’d highly recommend that you run the main longitudinal stream first

Re: [Freesurfer] Thalamic Nuclei {Disarmed}

External Email - Use Caution Dear Zheng, You’ll need a more recent dev version to use the thalamic nucle segmentation. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff

Re: [Freesurfer] hippocampus subfield division

External Email - Use Caution Dear Yixin, Yes, give segmentHA_T1.sh a shot. You need to install the development version of FreeSurfer, though. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London

Re: [Freesurfer] Thalamic segmentation questions

External Email - Use Caution Dear Manoj, First question: The one without the suffix is defined at higher resolution, on a voxel grid that does not correspond to the standard FS space (where norm.mgz, aseg.mgz, etc. live). The one with the suffix lives on the voxel grid of

Re: [Freesurfer] Hippocampus subfield division error

External Email - Use Caution Thanks, Yixin. It just ran to completion on my machine with FreeSurfer 6.0. Let me know if you want me to send you the output. Did you notice this problem on other subjects? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre

Re: [Freesurfer] Hippocampus subfield division error

External Email - Use Caution Thanks! Can you please upload one of the subjects that fail? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff Martinos Center for Biomedical

Re: [Freesurfer] Hippocampus subfield division error

External Email - Use Caution Hi Yixin, Does this happen for all subjects, or only one? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff Martinos Center for Biomedical Imaging

Re: [Freesurfer] Longitudinal subfields segmentation single time point

External Email - Use Caution Thanks a lot for your email, Saskia. Does this happen for more than one subject? Can you reproduce the error? Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research

Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

Hippocampal Subfields - error during segmentation {Disarmed} External Email - Use Caution Version 6.0 Thanks, Rachel From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: Monday, January 7, 2019 2:50:57 AM

Re: [Freesurfer] Longitudinal Hippocampal Subfields - error during segmentation {Disarmed}

External Email - Use Caution Hi Rachel This is very weird. What exact version are you using? 6.0 or dev? Cheers Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London Research staff Martinos Center for

Re: [Freesurfer] thalamus_proper or whole_thalamus volume measurement?

External Email - Use Caution Dear Corinna, The reason for this is that the volumes correspond to two different analyses. The volumes from the two sources are highly correlated, though, so it shouldn’t make almost any difference to use one or the other – but it you’re doing any

Re: [Freesurfer] Classification of amygdala subregions using Freesurfers new Algorithm

December 2018 at 16:31 To: "freesurfer@nmr.mgh.harvard.edu" Cc: "Iglesias Gonzalez, Eugenio" Subject: Classification of amygdala subregions using Freesurfers new Algorithm Dear Eugenio and experts, I have run the segmentation of the hippocampus subfields and nuclei of the amygd

Re: [Freesurfer] segmentHA_T2 newbie questions

External Email - Use Caution Dear K 1. No 2. No, just the subject name; the subjects directory is specified separately. 3. Points at a file. 4. Yes. Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University

Re: [Freesurfer] Segmentation of hippocampal subfields on FS v6 stable data?

External Email - Use Caution Nope, please don't rerun the recon-all with dev. Just run the hippo+amyg module on the 6.0-reconned data. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London, and

Re: [Freesurfer] hippocampal subfield question

External Email - Use Caution Dear Arkadiy, Technically you should do it after, but the changes will be tiny, so it’s probably fine to do it before (as long as you’re consistent across subjects). Cheers, /E -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical

Re: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.

data of patient A to recon-all and T2 data of another patient B to segment ? Thank you very much. Confused beginner. Qimo At 2018-11-26 23:45:17, "Iglesias Gonzalez, Eugenio" wrote: External Email - Use Caution Dear Qimo, You do need a T1 vol

Re: [Freesurfer] segmentHA_T2.sh: amygdala recon-all command stoped.

External Email - Use Caution Dear Qimo, You do need a T1 volume to run the main recon-all; sorry if the wiki wasn’t clear enough. It is true that segmenta_T2.sh only uses the intensities of the FLAIR scan, but a recon-all processed T1 is still necessary. Cheers, /E -- Juan

Re: [Freesurfer] thalamic nuclei additional scan error

External Email - Use Caution Dear Zhac, Apologies for the mistake in the wiki. As explained in the error message, the subjects directory is the second argument. Also, if you are using a T2 scan, I would replace t1 by t2 in the last argument. The call should be: (For a T1

Re: [Freesurfer] loading and rendering the Amygdala nuclei only in Freeview

External Email - Use Caution Hi Erik, If you render labels >7000, you shouldn’t see a rendering of the subfields – but they will indeed remain visible in the orthogonal views. If you want to get rid of them, you can use mri_threshold: mri_threshold

Re: [Freesurfer] Longitudinal brainstem structures / thalamic nuclei

External Email - Use Caution Hi Niels, There is, but not in the short term. For the time being, you can run the module on longitudinally processed subjects. Cheers, /Eugenio -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and

Re: [Freesurfer] Segmentation of thalamic nuclei - no reticular nucleus

External Email - Use Caution Hi HSK We use it in the model fitting but do not segment it due to the absolute lack of contrast with the white matter. Kind regards, Eugenio -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and

Re: [Freesurfer] Matlab Segmentation error when running hippocampal segmentation in dev version

External Email - Use Caution Hi Jaime, Can you please send us the output you get between calling the command and the error? Cheers, /E -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College

Re: [Freesurfer] segmentHA_T1 error DYLD_LIBRARY_PATH

External Email - Use Caution It seems it could be a version conflict. Please try unsetting DYLD_LIBRARY_PATH. Cheers, /Eugenio -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file {Disarmed}

: cannot find transform file Hi, Looks like the input is a multi frame image. Should only be single frame. Best Martin On 26. Oct 2018, at 13:52, Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: It seems like a problem with mri_robust_register. Martin, any ideas? -- Juan E

Re: [Freesurfer] error in hippocampal subfields and nuclei of amygdala segmentation

External Email - Use Caution Dear J How much RAM memory do you have? Andrew: do you think this might be the problem? Cheers E Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 오진영

Re: [Freesurfer] subfield normalization vs. covarying for whole hippocampal volume

External Email - Use Caution Dear Lauren, This is a very interesting question! Site harmonization matters aside (there’s a vast literature on it), whether you correct by ICV or whole hippocampal volume essentially answers to different questions: - ICV: you’re asking whether

Re: [Freesurfer] Error in segmentHA_T1.sh

External Email - Use Caution No worries! Your LD_LIBRARY_PATH configuration made my day  -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com From: on

Re: [Freesurfer] segmentHA_T2.sh issue, ERROR: cannot find transform file

External Email - Use Caution It seems like a problem with mri_robust_register. Martin, any ideas? -- Juan Eugenio Iglesias Centre for Medical Image Computing (CMIC) Department of Medical Physics and Biomedical Engineering University College London http://www.jeiglesias.com

Re: [Freesurfer] Disjointed thalamic nuclei segmentation

for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: Niels Bergsland Date: Wednesday, 10 October 2018 at 15:42 To: "Iglesias Gonzalez, Eugenio" Subject: Re: [Freesurfer] Disjointed thalamic nuclei segmentation Hi Eugen

Re: [Freesurfer] Disjointed thalamic nuclei segmentation

External Email - Use Caution Thanks, Niels. I suspect the problem is that, for some reason, such voxels have much brighter intensity than their surroundings, and are classified as white matter / reticular nucleus. But that shouldn’t be happening that far from the lateral

Re: [Freesurfer] Fwd: Hippocampal-Amygdala subfields error

this. - Regarding the second question: it is a really good one. Would you mind posting it on the FreeSurfer list? Short answer is: same machine. Best -- Forwarded message - From: Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> Date: mié., 10 oct. 2018 a las 11:53 Subje

Re: [Freesurfer] Thalamic Nuclei segmentation results

External Email - Use Caution Hi Vasudev, What lookup table are you using to visualize the results? Are you using FreeView from the development version, and visualizing the segmentation with the default lookup table? Cheers, /Eugenio Juan Eugenio Iglesias Centre for Medical

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 segmentation with an additional scan ERROR kvlGEMSMatlab

with the additional high resolution scan works! Thank you for all the help! Pradeep On Thu, Oct 4, 2018 at 11:28 AM Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution Thanks! Did you check whether the T2 and the T1 were correctly registere

Re: [Freesurfer] Hippocampal/Amygdala subfield segmentation error - Freesurfer devel-20180612

External Email - Use Caution Hi Sally, It is indeed the linear registration used to initialize the atlas deformation that is going crazy. Do you think you could upload the subject, so we can take a look? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow

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

scan ERROR kvlGEMSMatlab External Email - Use Caution I have tried this for two subjects and got the same error. Thanks, Pradeep On Thu, Oct 4, 2018 at 11:14 AM Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>> wrote: External Email - Use Caution Dear Pradeep, D

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

External Email - Use Caution Dear Pradeep, Did you get this error on several subjects, or only one? 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 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] amygdala segmentation atlas influence

London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: "Dr Rajendra Morey, M.D." Date: Monday, 1 October 2018 at 21:53 To: "Iglesias Gonzalez, Eugenio" , Freesurfer support list Subject: RE: [Freesurfer] amygdala segmentation atlas influence Hi Eugenio Than

Re: [Freesurfer] cannot stat volumesAmygdala.txt

, 30 September 2018 at 22:15 To: Freesurfer support list Subject: Re: [Freesurfer] cannot stat volumesAmygdala.txt External Email - Use Caution Hi it is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c John On Sun, Sep 30, 2018 at 2:50 PM Iglesias Gonzalez, Eugenio

Re: [Freesurfer] amygdala segmentation atlas influence

External Email - Use Caution Dear Raj, A few years ago, we published a paper on how Monte Carlo sampling could be used to quantify this. Unfortunately, the method was incredibly slow and difficult to tune, and the performance gain was tiny, so we never put it in FreeSurfer. But

Re: [Freesurfer] cannot stat volumesAmygdala.txt

External Email - Use Caution Hi Jon, What exact version are you using? Is it a recent development version? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com

Re: [Freesurfer] matlab MEXFile error in thalamic nuclei segmentation script

External Email - Use Caution Hi Carme, This has to do with the CentOS version. Please try the version compiled on CentOS6 (that should fix the problem). Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University

Re: [Freesurfer] Hippocampal-Amygdala subfields error

the log file /Applications/freesurfer/subjects/5095/scripts/hippocampal-subfields-T2.HIPO-AMI.log What could be the problem? Thanks in advance, Best wishes, El vie., 14 sept. 2018 a las 0:40, Iglesias Gonzalez, Eugenio (mailto:e.igles...@ucl.ac.uk>>) escribió: External Emai

Re: [Freesurfer] Hippocampal-Amygdala subfields error

External Email - Use Caution Hi Miguel Angel, This bug was recently fixed in the dev version. If you download the most recent one, you won’t have this problem. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC)

Re: [Freesurfer] Minimum FS version for thalamic segmentation

External Email - Use Caution Hi Niels 5.1 should do but please let us know if it doesn't! Cheers E Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Niels Bergsland Sent: Wednesday,

Re: [Freesurfer] Amygdala subfields segmentation

-dev.tar.gz Thanks in advance, Best, El mar., 11 sept. 2018 a las 17:47, Iglesias Gonzalez, Eugenio (mailto:e.igles...@ucl.ac.uk>>) escribió: External Email - Use Caution Dear MA Please download the latest dev version and the command will be there Cheers Eugenio Sent from my

Re: [Freesurfer] Amygdala subfields segmentation

External Email - Use Caution Dear MA Please download the latest dev version and the command will be there Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Miguel Ángel

Re: [Freesurfer] Using the new Thalamus tool

appreciated. Cheers Erik From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Iglesias Gonzalez, Eugenio Sent: 10 September 2018 18:00:20 To: freesurfer@nmr.mgh.harvard.edu; Freesurfer support list Subject: Re: [Freesurfer] Using the new Thalamus tool

Re: [Freesurfer] thalamic segmentation

External Email - Use Caution Hi Vinny, The anatomical definitions can be found in the paper, which is open access (see Table 2): https://www.sciencedirect.com/science/article/pii/S1053811918307109 Kind regards Eugenio Sent from my phone, please excuse brevity and typos

Re: [Freesurfer] amygdala segmentation using additional scan error

External Email - Use Caution Hi Jinyoung Sorry for the slow response but I'm traveling these days I believe this is a bug that was fixed in the dev version 2-3 weeks ago. Would you mind trying the latest dev, and checking whether that solves the problem? Cheers Eugenio Sent from

Re: [Freesurfer] Using the new Thalamus tool

External Email - Use Caution Dear Erik, Installing only the thalamic tool is technically possible but requires a level of hacking that i don't want to encourage or support ;-) Please install the new dev on a separate directory, and make FREESURFER_HOME point to that the

Re: [Freesurfer] hippocampus subfields with T2

External Email - Use Caution Um this is an empirical question. I would try with and without, and then decide. Cheers Eugenio Sent from my phone, please excuse brevity and typos From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of

Re: [Freesurfer] questions about hippocampus subfield error

is all log file within script directory. Would you please help me to figure out what was wrong? Thank you so much Best wishes Shize 在 2018-08-24 15:50:44，"Iglesias Gonzalez, Eugenio" 写道： External Email - Use Caution I am really confused. There are no errors in the subfi

Re: [Freesurfer] questions about hippocampus subfield error

:08:35，"Iglesias Gonzalez, Eugenio" 写道： External Email - Use Caution Thanks! Can you please send us the log of the hippocampal subfield segmentation? It should be in the same directory as the recon-all log. Cheers, /E Juan Eugenio Iglesias Centre for Medical Image Compu

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution Hi Eugenio, Yes, If I run without the hippocampal subfield flag. Recon-all complete without any error. So I am confused what is wrong with this. Thank you Shize 在 2018-08-24 00:02:32，"Iglesias Gonzalez, Eugenio" 写道： External Email - Use C

Re: [Freesurfer] questions about hippocampus subfield error

External Email - Use Caution Hi Shize, Does recon-all complete when you run it without the hippocampal subfield flag? It doesn’t look like an error in the subfield module to me … Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image

Re: [Freesurfer] hippocampal subfield segmentation

External Email - Use Caution Hi Ryan, Is it possible that you're mixing versions of FreeSurfer in your PATH and/or LD_LIBRARY_PATH? Maybe you could try unsetting them before you source FreeSurfer? Cheers, /Eugenio Juan Eugenio Iglesias Centre for Medical Image Computing

Re: [Freesurfer] segmentHA_T1.sh exits with error

External Email - Use Caution Dear Antonin, Thanks again for letting us know you had this problem; it turned out to be a small, silly bug in the code. I will fix it ASAP, and the updated code should be on the dev version in the next few days. Cheers, /Eugenio -- Juan Eugenio

Re: [Freesurfer] Freesurfer v6.0: Using FLAIR for hippocampal subfields

External Email - Use Caution Without having seen your FLAIR scans, I’d say probably not, but it’s an empirical question; give them a go! ;-) -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London

Re: [Freesurfer] segmentHA_T1.sh exits with error

External Email - Use Caution Dear Antonin, Can you please send me a listing of the files in: /hydra-db/hydra_io/vypocty/freeSurfer/A_analysis_HPC_PFC/A_links_all/ESO_C00577_20160303_1246_1/tmp/hippoSF_T1_v21_right/ Kind regards, /Eugenio -- Juan Eugenio Iglesias ERC Senior

Re: [Freesurfer] Hippocampal subfield registration question.

External Email - Use Caution Hi Jamie, It’s a message from mri_robust_register in the initialization of the atlas position. If the finaloutput looks reasonable (which it mostly likely will), don’t worry too much. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research

[Freesurfer] New segmentation of thalamic nuclei

External Email - Use Caution Dear FreeSurfer users, It is my pleasure to announce that our new tool to segment the thalamic nuclei from structural MR scans is available in the development version of FreeSurfer. The tool relies on an atlas derived from manual annotations made on

Re: [Freesurfer] Mismatching hippocampal output

External Email - Use Caution Hi Sophie. No output is better than the other. If you have run all your subjects with both, I'd say to take the average! Sent from my phone, please excuse brevity and typos From:

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

External Email - Use Caution Dear Vasudev, It is expected that you get different volume estimates with different atlases (FreeSurfer vs CobraLab), as the manual delineation protocols that were used to create them are very different (e.g., see Yushkevich et al., NeuroImage,

Re: [Freesurfer] hippocampal subfields segmentation error

0 Iglesias Gonzalez, Eugenio mailto:e.igles...@ucl.ac.uk>>: 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

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] Label numbers for thalamic nuclei

External Email - Use Caution Dear KT, They range from 8100 to 8300. Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf

Re: [Freesurfer] Re?? Re?? Re??segmentHA_T2.sh

tHA_T1.sh subject003", it's well done! When run Thanks, Fiona -- ------ ??: "Iglesias Gonzalez, Eugenio"; : 2018??7??18??(??) 8:35 ??: "Freesurfer support list";"Freesurfersupport list"; : Re: [Frees

Re: [Freesurfer] Re?? Re??segmentHA_T2.sh

3 days. No error reported here. Thanks , Fiona Ding. -- -- ??????: "Iglesias Gonzalez, Eugenio"; : 2018??7??18??(??) 7:29 ??: "Freesurfer support list"; : Re: [Freesurfer] Re??segmentHA_T2.sh External Email -

Re: [Freesurfer] Re：segmentHA_T2.sh

External Email - Use Caution Thanks, Fiona. Is the error reproducible? Does it always die at the same step? Do you get the same problem with other subjects? Cheers, /Eugenio -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University

Re: [Freesurfer] segmentHA_T2.sh

External Email - Use Caution Weird! Maybe you ran out of RAM memory? -- Juan Eugenio Iglesias ERC Senior Research Fellow Centre for Medical Image Computing (CMIC) University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ From: on behalf of 墨初

  1   2   3   >