External Email - Use Caution
We calculated p-value/tstat overlays using FSL PALM comparing the
cortical thickness of different groups. We aim for a measure of
similarity in cortical thickness between some of the groups. Our idea
was to use dice overlap between groups to test similarity in atrophy
patterns.
We tried to use ‚mri_compute_overlap‘ to obtain these measures but
when we used the p-value overlays we found that mrs_compute_overlap
returned us the dice overlap for cortical regions and also white
matter and unknown labeled regions what is not expected in a cortical
thickness stats map I guess. So we doubt that is the correct way to
use these overlays.
Do you have any idea how to calculate the dice overlap of statistical
overlays (vertex wise)?
Thanks,
Ersin Ersözlü
<freesurfer-requ...@nmr.mgh.harvard.edu
<mailto:freesurfer-requ...@nmr.mgh.harvard.edu>> adresine sahip
kullanıcı 9 Nis 2020 Per, 18:01 tarihinde şunu yazdı:
Send Freesurfer mailing list submissions to
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When replying, please edit your Subject line so it is more specific
than "Re: Contents of Freesurfer digest..."
Today's Topics:
1. Re: Error in Tracula-all -prep (Yendiki, Anastasia)
2. Re: Tracula: tract length meaning (Yendiki, Anastasia)
3. Re: Hippocampal Subfield Segmentation Error
(Lab of Autism and Developmental Neuroscience, Lab of
Autism and Developmental Neuroscience)
4. Re: mri_convert input files (Douglas N. Greve)
5. Re: mri_glmfit-sim FWHM error (Douglas N. Greve)
6. Re: Aseg file issue (Douglas N. Greve)
7. Overlap of vertices in downsampled data (Ersin Ers?zl?)
8. Re: Overlap of vertices in downsampled data (Douglas N. Greve)
9. Re: Fwd: Is it possible to load flatmaps in freeview and draw
ROI's on them? (Ruopeng Wang)
10. Re: Aseg file issue
(Lab of Autism and Developmental Neuroscience, Lab of
Autism and Developmental Neuroscience)
----------------------------------------------------------------------
Message: 1
Date: Thu, 9 Apr 2020 02:34:53 +0000
From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu
<mailto:ayend...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Error in Tracula-all -prep
To: "freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<mn2pr04mb575785a35596bd0bb37bf85a8a...@mn2pr04mb5757.namprd04.prod.outlook.com
<mailto:mn2pr04mb575785a35596bd0bb37bf85a8a...@mn2pr04mb5757.namprd04.prod.outlook.com>>
Content-Type: text/plain; charset="us-ascii"
Hi Salah - It looks like it didn't find your subject's freesurfer
recon when it was doing the pre-processing, so it skipped some
steps that you need to go beyond that point. Based on your
SUBJECTS_DIR and your subject name, it looked for this file:
/Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/mri/brain.mgz
Any chance this was missing or unreadable?
a.y
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of
Salah Showiheen <sshowih...@gmail.com <mailto:sshowih...@gmail.com>>
Sent: Monday, April 6, 2020 11:49 PM
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Error in Tracula-all -prep
External Email - Use Caution
Hi Freesurfer community,
I have an issue that I spent ages trying to figure out and this
error has been asked about back in (17/12/2016) and the title is
([Freesurfer] Tracula trac -all preprocessing error.
my error is:
ERROR: fio_pushd:
/Volumes/HD/Post_HARDI/PAH_Clinical_110/07/C07/dlabel/mni
There is an issue that the mini folder is empty.
Attached is the log file and the configuration file (tracula_conf.txt)
Regards,
Salah
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Message: 2
Date: Thu, 9 Apr 2020 02:39:35 +0000
From: "Yendiki, Anastasia" <ayend...@mgh.harvard.edu
<mailto:ayend...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Tracula: tract length meaning
To: "freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<mn2pr04mb5757d0b4e6676203698545588a...@mn2pr04mb5757.namprd04.prod.outlook.com
<mailto:mn2pr04mb5757d0b4e6676203698545588a...@mn2pr04mb5757.namprd04.prod.outlook.com>>
Content-Type: text/plain; charset="iso-8859-3"
Hi Nazife - That is correct, the lengths are numbers of voxels
along a tract in each subject's native DWI space, so if you were
to compare them across subjects you'd probably want to correct for
total intracranial volume. (This is just as you would do for any
other length/area/volume measurement derived in individual space,
like cortical thickness, etc.) Let me know if you have any other
questions!
a.y
________________________________
From: freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of
Nazife Ayy?ld?z <nazifeayyil...@gmail.com
<mailto:nazifeayyil...@gmail.com>>
Sent: Wednesday, April 8, 2020 8:43 AM
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula: tract length meaning
External Email - Use Caution
Dear Tracula experts,
I want to compare two groups according to the length statistics
from Tracula overall.stats outputs. I just need comprehensive
explanations what "tract length" statistics mean and how they are
derived and what their reliability is. I checked but I couldn't
find detailed information.
Are they suitable to use in group comparisons? If so, which one is
more suitable to use: average, center, min or max length? I saw in
some articles that they used average_length of a tract. If I want
to use length statistics do you suggest taking any control variables?
I read a message from Anastasia in the archive-list saying that we
should be aware that these measures are in their individual DWI
spaces. If I understood correctly, I shouldn't use them directly.
Should I control the head sizes of the individuals then? How would
you do if you wanted to do this kind of comparative analysis?
I would really appreciate it if you answer. Thank you very much in
advance!
Best regards,
Nazife
--
-Nazife Ayy?ld?z-
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------------------------------
Message: 3
Date: Wed, 8 Apr 2020 23:25:25 -0400
From: "Lab of Autism and Developmental Neuroscience, Lab of
Autism and
Developmental Neuroscience" <l...@email.gwu.edu
<mailto:l...@email.gwu.edu>>
Subject: Re: [Freesurfer] Hippocampal Subfield Segmentation Error
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<CACE7MBLy55HWz_51M_eP8cN41aVYd9S1fRfD=jQ0x=lrbob...@mail.gmail.com
<mailto:lrbob...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello!
So I have installed the latest Java, reinstalled the Runtime
following the
instructions on the Freesurfer website, and have attempted to remove
Java.opts files, to then run the analysis. Still nothing has
changed. Any
other suggestions?
Thank you,
Alex
On Tue, Mar 31, 2020 at 6:17 PM Iglesias Gonzalez, Juan E. <
jiglesiasgonza...@mgh.harvard.edu
<mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote:
> Uuuummm this is a tough one. Any ideas, Andrew? Maybe updating java?
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Lab of
> Autism and Developmental Neuroscience, Lab of Autism and
Developmental
> Neuroscience" <l...@email.gwu.edu <mailto:l...@email.gwu.edu>>
> *Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
> *Date: *Tuesday, March 31, 2020 at 17:59
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
> *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error
>
>
>
> * External Email - Use Caution *
>
> Hello Eugenio,
>
> No I wasn't! When I first tried to run the subfields I wasn't
pointed to
> downloading a version of Java. I do have Java on the MAC I'm
using, but the
> error "unable to start JVM because of a bad java option" still
appears. Any
> other ideas on how to fix this?
>
> Thanks,
>
> Alex
>
>
>
> On Mon, Mar 30, 2020 at 10:12 AM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu
<mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote:
>
> HI Alex,
>
> Were you pointed to downloading a version of Java when you first
tried to
> run
>
> the subfields? If so, did you follow the instructions?
>
> Cheers,
>
> /Eugenio
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Lab of
> Autism and Developmental Neuroscience, Lab of Autism and
Developmental
> Neuroscience" <l...@email.gwu.edu <mailto:l...@email.gwu.edu>>
> *Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
> *Date: *Saturday, March 28, 2020 at 02:07
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
> *Subject: *Re: [Freesurfer] Hippocampal Subfield Segmentation Error
>
>
>
> * External Email - Use Caution *
>
> Dear Freesurfer experts,
>
>
>
> Hope everyone is well! I'm unfortunately continuing to have
errors running
> the hippocampal subfield segmentation. Apparently it's being
caused by
> issues with the java.opts files. I tried removing it (as
recommended by a
> link someone set me from the Matlab help website), but it made no
> difference. Please find my code and error message below:
>
>
>
>
>
>
>
> CCASPH-A1900447:3003 ajobsaid$ recon-all -s Sub_42
> -hippocampal-subfields-T1
>
> Subject Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>
> Current Stamp: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>
> INFO: SUBJECTS_DIR is /Applications/freesurfer/BAP/3003
>
> Actual FREESURFER_HOME /Applications/freesurfer
>
> -rw-rw-r-- 1 ajobsaid wheel 859204 Mar 24 12:59
> /Applications/freesurfer/BAP/3003/Sub_42/scripts/recon-all.log
>
> Darwin CCASPH-A1900447.cloud.ccas.gwu.edu
<http://CCASPH-A1900447.cloud.ccas.gwu.edu> 18.7.0 Darwin Kernel
Version
> 18.7.0: Thu Jan 23 06:52:12 PST 2020;
root:xnu-4903.278.25~1/RELEASE_X86_64
> x86_64
>
> #--------------------------------------------
>
> #@# Hippocampal Subfields processing (T1 only) left Tue Mar 24
15:09:44
> EDT 2020
>
> \n /Applications/freesurfer/bin/segmentSF_T1.sh
> /Applications/freesurfer/MCRv80 /Applications/freesurfer Sub_42
> /Applications/freesurfer/BAP/3003 left \n
>
> See log file:
>
/Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log
>
> ------------------------------------------
>
> Setting up environment variables
>
> ---
>
> DYLD_LIBRARY_PATH is
>
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
>
> Warning: application is running on a locale different from the
original
> platform locale.
>
> JavaVM: Failed to load JVM:
>
/Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib
>
> JavaVM FATAL: Failed to load the jvm library.
>
> 2020-03-24 15:09:45.262
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.263
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.263
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.264
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.264
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.264
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.265
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.265
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:45.265
> segmentSubjectT1_autoEstimateAlveusML[66267:3452922] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> JavaVM: Failed to load JVM:
>
/Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib
>
> JavaVM FATAL: Failed to load the jvm library.
>
> Fatal Error on startup: Unable to start the JVM because of a bad
Java
> option or unknown error.
>
>
>
> #--------------------------------------------
>
> #@# Hippocampal Subfields processing (T1 only) right Tue Mar 24
15:09:45
> EDT 2020
>
> \n /Applications/freesurfer/bin/segmentSF_T1.sh
> /Applications/freesurfer/MCRv80 /Applications/freesurfer Sub_42
> /Applications/freesurfer/BAP/3003 right \n
>
> See log file:
>
/Applications/freesurfer/BAP/3003/Sub_42/scripts/hippocampal-subfields-T1.log
>
> ------------------------------------------
>
> Setting up environment variables
>
> ---
>
> DYLD_LIBRARY_PATH is
>
.:/Applications/freesurfer/MCRv80/runtime/maci64:/Applications/freesurfer/MCRv80/bin/maci64:/Applications/freesurfer/MCRv80/sys/os/maci64:
>
> Warning: application is running on a locale different from the
original
> platform locale.
>
> JavaVM: Failed to load JVM:
>
/Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib
>
> JavaVM FATAL: Failed to load the jvm library.
>
> 2020-03-24 15:09:46.333
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.334
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.334
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.334
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.335
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.335
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.336
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.336
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> 2020-03-24 15:09:46.336
> segmentSubjectT1_autoEstimateAlveusML[66303:3453013] This process is
> attempting to exclude an item from Time Machine by path without
> administrator privileges. This is not supported.
>
> JavaVM: Failed to load JVM:
>
/Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib
>
> JavaVM FATAL: Failed to load the jvm library.
>
> Fatal Error on startup: Unable to start the JVM because of a bad
Java
> option or unknown error.
>
>
>
>
>
> Started at Tue Mar 24 15:09:43 EDT 2020
>
> Ended at Tue Mar 24 15:09:46 EDT 2020
>
> #@#%# recon-all-run-time-hours 0.001
>
> recon-all -s Sub_42 finished without error at Tue Mar 24
15:09:46 EDT 2020
>
>
>
> Hopefully someone has an idea of what could be done next. Thanks!
>
>
>
> All the best,
>
> Alex
>
>
>
> On Sun, Mar 22, 2020 at 10:57 AM Iglesias Gonzalez, Juan E. <
> jiglesiasgonza...@mgh.harvard.edu
<mailto:jiglesiasgonza...@mgh.harvard.edu>> wrote:
>
> Dear Alex,
>
> Can you please try this?
>
>
>
https://uk.mathworks.com/matlabcentral/answers/196961-why-do-i-receive-fatal-error-on-startup-unable-to-start-the-jvm-because-of-a-bad-java-option-or-un
>
> Cheers,
>
> /E
>
>
>
>
>
> Juan Eugenio Iglesias
>
> Senior research fellow
>
> CMIC (UCL), MGH (HMS) and CSAIL (MIT)
>
> http://www.jeiglesias.com
>
>
>
>
>
>
>
> *From: *<freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Lab of
> Autism and Developmental Neuroscience, Lab of Autism and
Developmental
> Neuroscience" <l...@email.gwu.edu <mailto:l...@email.gwu.edu>>
> *Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
> *Date: *Saturday, March 21, 2020 at 23:33
> *To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
> *Subject: *[Freesurfer] Hippocampal Subfield Segmentation Error
>
>
>
> * External Email - Use Caution *
>
> Dear Freesurfer experts,
>
>
>
> I am having a problem with hippocampal subfield segmentation.
The issue
> appears to be related to JavaVM - after I run the code: recon-all -s
> (subject ID) -hippocampal-subfields-T1
>
> This is the error:
>
>
>
> JavaVM: Failed to load JVM:
>
/Library/Java/JavaVirtualMachines/adoptopenjdk-13.jdk/Contents/Home/bundle/Libraries/libserver.dylib
>
> JavaVM FATAL: Failed to load the jvm library.
>
> Fatal Error on startup: Unable to start the JVM because of a bad
Java
> option or unknown error.
>
> Please check your java.opts file.
>
> Any suggestions?
>
>
>
> Thank you,
>
> Alex
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 4
Date: Thu, 9 Apr 2020 10:34:11 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_convert input files
To: <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <8c74a8a1-d643-a6ff-f097-1834c4a94...@mgh.harvard.edu
<mailto:8c74a8a1-d643-a6ff-f097-1834c4a94...@mgh.harvard.edu>>
Content-Type: text/plain; charset="windows-1252"
Sorry, we can't convert PAR/REC files.
On 4/8/2020 4:20 AM, Setiaman, N. wrote:
>
> ????????External Email - Use Caution
>
> Hi,
>
> I would like to convert my raw scans to nifty. The scans are
made on a
> Philips scanner. I was able to retrieve most of them as DICOM
files,
> but some of them are only available as PAR/REC. Does mri_convert
also
> handle PAR/REC or can I only convert the DICOMS with this tool?
>
> Best,
>
> Nikita
>
>
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Message: 5
Date: Thu, 9 Apr 2020 10:35:20 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] mri_glmfit-sim FWHM error
To: <s7675...@stud.uni-frankfurt.de
<mailto:s7675...@stud.uni-frankfurt.de>>, Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <e69bbb84-3362-5cf8-3d80-a56df1e13...@mgh.harvard.edu
<mailto:e69bbb84-3362-5cf8-3d80-a56df1e13...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"; format=flowed
Did you down load all the files in the patch? I think the new
mri_surfcluster is there
On 4/8/2020 8:51 AM, s7675...@stud.uni-frankfurt.de
<mailto:s7675...@stud.uni-frankfurt.de> wrote:
> External Email - Use Caution
> Hi again,
> I already took a few more steps and set up PALM/ fspalm. It's
working
> fine, up to the point where it does the actual cluster analysis. As
> part of the script, the command
> mri_surfcluster --in fsp_clustere_tstat_fwep.mgz --thmin 1.301030
> --subject fsaverage --hemi lh --annot aparc --sum resilience.
> clustertable.summary --no-fixmni --surf white --ocn
resilience.ocn.mgz
> oannot ./resilience.ocn.annot --sig2pmax --bonferroni-max2
> is generated. However, the last two flags (--sig2pmax
> --bonferroni-max2) are not recognized, so it crashes. Indeed,
they do
> not appear as possible flags in the mri_surfcluster --help
section, so
> how and why do they get here...?
> Just to see what happens, I ran the mri_surfcluster... command
without
> the last 2 flags, which only gave me another error: "could not read
> fsp_clustere_tstat_fwep.mgz as type"
>
> Do you have an idea what I could do about this?
> Thanks a lot,
> Doro
>
> Zitat von s7675...@rz.uni-frankfurt.de
<mailto:s7675...@rz.uni-frankfurt.de>:
>
>> Hi Douglas,
>>
>> I just saw that permutation wasn't working for me because I use
>> continuous covariates/ a non-orthogonal design. You just
answered to
>> a similar question in the mailing list yesterday and suggested
to add
>> "--perm-resid", but this flag does not exist for the
mri_glmfit-sim
>> command, does it? Do I have to install PALM to be able to run
>> permutation on my design or is there any way around that?
>>
>> Thanks again,
>>
>> Doro
>> Zitat von "Douglas N. Greve" <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>:
>>
>>> On 4/6/2020 10:57 AM, s7675...@stud.uni-frankfurt.de
<mailto:s7675...@stud.uni-frankfurt.de> wrote:
>>>> External Email - Use Caution
>>>> Hi Douglas,
>>>>
>>>> thanks a lot for your quick response. I wanted to use Monte
Carlo sim
>>>> as all other analyses in our project include a monte carlo
simulation
>>>> and I try to keep things consistent. Am I getting you right -
there is
>>>> no way to run a monte carlo simulation with LGI data? And why
exactly
>>>> would you not recommend it in this case (even if it worked)?
>>> Yes, you can do the MCZ simulation yourself with mri_mcsim,
>>> something like
>>> mri_mcsim --o /your/space/mcsim/fsaverage/lh/cortex --base mc-z
>>> --save-iter --surf fsaverage lh --nreps 1000 --fwhm 37
>>> Then run mri_glmfit-sim as you did before, but specify
--mczsim-dir
>>> /your/space/mcsim
>>>
>>>>
>>>> I did try permutations with freesurfer in the past, but it never
>>>> really worked out for me, to be honest. They kept running for
ages and
>>>> I stopped them after 6-7 days...
>>> Not sure what happened, but if you want to debug it, I can help
>>>
>>>>
>>>> Thanks in advance,
>>>>
>>>> Doro
>>>> Zitat von "Douglas N. Greve" <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>:
>>>>
>>>>> The problem is that mri_glmfit-sim is looking for a entry in the
>>>>> table that does not exist. The table only goes up to a
smoothness
>>>>> level of 35. LGI data tend to bed very smooth. I would strongly
>>>>> recommend that you use permutation instead. See
>>>>>
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm
>>>>>
>>>>>
>>>>> On 4/6/2020 7:42 AM, s7675...@stud.uni-frankfurt.de
<mailto:s7675...@stud.uni-frankfurt.de> wrote:
>>>>>> External Email - Use Caution
>>>>>> Dear Freesurfer experts,
>>>>>>
>>>>>> I'm trying to run a simulation (--> mri_glmfit-sim) with
cached LGI
>>>>>> data (fwhm10), but get an error due to the estimated fwhm
kernel.
>>>>>> The folder corresponding to the fwhm value (-->37) does not
exist, I
>>>>>> guess because it's a pretty unusual value...?
>>>>>>
>>>>>> DoSim = 0
>>>>>> UseCache = 1
>>>>>> DoPoll = 0
>>>>>> DoPBSubmit = 0
>>>>>> DoBackground = 0
>>>>>> DiagCluster = 0
>>>>>> gd2mtx = dods
>>>>>> fwhm = 36.855100
>>>>>> ERROR: cannot find
>>>>>>
/apps/prod/x86_64/freesurfer-6.0.1/average/mult-comp-cor/fsaverage/lh/cortex/fwhm37/abs/th20/mc-z.csd
>>>>>>
>>>>>>
>>>>>> I've seen mails describing similar issues in the archive
and from
>>>>>> your explanation I more or less understand that you cannot
define
>>>>>> this value as it is estimated in the process...? However, I
did not
>>>>>> see if there is a solution to this problem. What could I do
about it
>>>>>> now?
>>>>>>
>>>>>> I attached the logfiles and would be very grateful for your
help,
>>>>>>
>>>>>> thanks a lot and stay healthy,
>>>>>>
>>>>>> Doro
>>>>>>
>>>>>> _______________________________________________
>>>>>> Freesurfer mailing list
>>>>>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
------------------------------
Message: 6
Date: Thu, 9 Apr 2020 10:36:22 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Aseg file issue
To: <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <4134342b-754b-57f3-2087-8ddeb1100...@mgh.harvard.edu
<mailto:4134342b-754b-57f3-2087-8ddeb1100...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"
Hi, unfortunately, QDEC is no longer being supported. Try using
mris_preproc and mri_glmfit with FSGD files.
On 4/8/2020 7:03 PM, Lab of Autism and Developmental Neuroscience,
Lab
of Autism and Developmental Neuroscience wrote:
>
> ????????External Email - Use Caution
>
> Dear Freesurfer experts,
>
> I'm having some difficulty importing my aseg stats data onto
QDEC. The
> error which I'm getting is seen below (please open the JPEG
file). Any
> ideas on why this?is happening? Thank you!
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 7
Date: Thu, 9 Apr 2020 17:01:53 +0200
From: Ersin Ers?zl? <ersinerso...@gmail.com
<mailto:ersinerso...@gmail.com>>
Subject: [Freesurfer] Overlap of vertices in downsampled data
To: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAA-=y9vG4PH-hC5P+0-003pVbJXmRo5uyC8TEokKKKQd68==d...@mail.gmail.com
<mailto:d...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hi FreeSurfer experts, We calculated the differences with downsampled
-fsaverage6- thickness data between our groups using 'PALM' on the
vertex
level and got .mgz files as overlays wit h log-p values for each
contrast.
Now, we would like to test the overlap. We computed a ratio of overlap
through 'mri_compute_overlap' within log-p overlay files but it showed
labels (-s option) such as unknown and white matter. Is there a way to
differentiate vertices that are in cortical regions? And could this
labeling be correct?
Medical doctoral student
University of Munich (LMU)
Ersin Ers?zl?
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Message: 8
Date: Thu, 9 Apr 2020 11:19:30 -0400
From: "Douglas N. Greve" <dgr...@mgh.harvard.edu
<mailto:dgr...@mgh.harvard.edu>>
Subject: Re: [Freesurfer] Overlap of vertices in downsampled data
To: <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID: <70162b3e-fabb-9728-0dd2-0105d8305...@mgh.harvard.edu
<mailto:70162b3e-fabb-9728-0dd2-0105d8305...@mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"
I can't tell from your description what you have done (or are
trying to
do). Can you elaborate?
On 4/9/2020 11:01 AM, Ersin Ers?zl? wrote:
>
> ????????External Email - Use Caution
>
> Hi FreeSurfer experts, We calculated the differences with
downsampled
> -fsaverage6- thickness data between our groups using 'PALM' on the
> vertex level and got .mgz files as overlays wit h log-p values for
> each contrast. Now, we would like to test the overlap. We
computed a
> ratio of overlap through 'mri_compute_overlap' within log-p overlay
> files but it showed labels (-s option) such as unknown and white
> matter. Is there a way to differentiate vertices that are in
cortical
> regions? And could this labeling be correct?
>
> Medical doctoral student
> University of Munich (LMU)
> Ersin Ers?zl?
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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------------------------------
Message: 9
Date: Thu, 9 Apr 2020 11:37:26 -0400
From: Ruopeng Wang <rpw...@nmr.mgh.harvard.edu
<mailto:rpw...@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] Fwd: Is it possible to load flatmaps in
freeview and draw ROI's on them?
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<f21c2b48-26f1-4b5f-b8b8-c70ca3044...@nmr.mgh.harvard.edu
<mailto:f21c2b48-26f1-4b5f-b8b8-c70ca3044...@nmr.mgh.harvard.edu>>
Content-Type: text/plain; charset="utf-8"
Hi Devavrat,
Freeview in FS 6.0 can?t load patches but the upcoming FS 7 can.
If you want to give it try, you can download the latest build from
here:
https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview
<https://surfer.nmr.mgh.harvard.edu/fswiki/UpdateFreeview>
To load a patch, run:
freeview -f lh.inflated:patch=patch_file
Best,
Ruopeng
> On Apr 7, 2020, at 9:24 PM, Devavrat Vartak PhD
<dvar...@berkeley.edu <mailto:dvar...@berkeley.edu>> wrote:
>
> External Email - Use Caution
>
>
> Hello Freesurfer developers,
>
> Thank you for developing Freesurfer!
>
> I am postdoc at UC Berkeley and I am using Freesurfer 6.0 to
create flat maps on which I draw my ROI's. The flat maps/patches
are created in TKSURFER.
> However, I typically use Freeview to visualise my volumes and
inflated surfaces, overlay data etc.
> I am trying to open flatmap maps in freeview but I am not able
to. I was wondering if it was possible to load flatmaps in
freeview and draw ROI's on them and overlay my data?
>
> OS: MacBook OS
>
> Thank you.
>
> Best,
> Devavrat
>
> --
> Devavrat Vartak, PhD
> Postdoctoral Researcher
>
> Helen Wills Neuroscience Institute and School of Optometry
>
> Mailing address:
> 360 Minor Hall #2020
> University of California, Berkeley
> Berkeley, CA, 94720-2020
> USA
>
> Website: www.dvartak.com <http://www.dvartak.com>
<http://www.dvartak.com/>
>
> Email:
> dvar...@berkeley.edu <mailto:dvar...@berkeley.edu>
<mailto:dvar...@berkeley.edu <mailto:dvar...@berkeley.edu>>
> devavratvar...@gmail.com <mailto:devavratvar...@gmail.com>
<mailto:devavratvar...@gmail.com <mailto:devavratvar...@gmail.com>>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 10
Date: Thu, 9 Apr 2020 11:40:19 -0400
From: "Lab of Autism and Developmental Neuroscience, Lab of
Autism and
Developmental Neuroscience" <l...@email.gwu.edu
<mailto:l...@email.gwu.edu>>
Subject: Re: [Freesurfer] Aseg file issue
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
Message-ID:
<CACE7MB+Uep=jvoxjk1ra-pqh0poer5kdi8_g2dje8rx+pty...@mail.gmail.com
<mailto:jvoxjk1ra-pqh0poer5kdi8_g2dje8rx%2bpty...@mail.gmail.com>>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Thank you for the information!
On Thu, Apr 9, 2020 at 10:38 AM Douglas N. Greve
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>>
wrote:
> Hi, unfortunately, QDEC is no longer being supported. Try using
> mris_preproc and mri_glmfit with FSGD files.
>
> On 4/8/2020 7:03 PM, Lab of Autism and Developmental
Neuroscience, Lab of
> Autism and Developmental Neuroscience wrote:
>
> External Email - Use Caution
> Dear Freesurfer experts,
>
> I'm having some difficulty importing my aseg stats data onto
QDEC. The
> error which I'm getting is seen below (please open the JPEG
file). Any
> ideas on why this is happening? Thank you!
>
>
>
> _______________________________________________
> Freesurfer mailing
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
<http://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
<mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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End of Freesurfer Digest, Vol 194, Issue 11
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