Re: [Freesurfer] mri_WMHsynthseg error: Killed 9

External Email - Use Caution Dr. Iglesias, I am still receiving the killed message. I am also stumped by how the platform was working for me not too long ago. I was able to run ~160 sequences recently without issue. Is there anything else I can try? Best, Ian Johnson, B.A

Re: [Freesurfer] mri_WMHsynthseg error: Killed 9

External Email - Use Caution Dr. Iglesias, Let me give it a try using that addition and I'll let you know if it fails again. Best, Ian Johnson, B.A. Clinical Research Associate Division of Neurocritical Care & Emergency Neurology Yale School of Medicine E: i

Re: [Freesurfer] error: Bad CPU type in executable WMH FreeSurfer

operating system name and revision running on the machine. - R. On Oct 7, 2024, at 16:13, Johnson, Ian wrote: External Email - Use Caution Hello Free Surfer Pros, I am trying to run WMH-Synth-Seg on a different machine (2.4GHz Quad-Core Intel Core i5, Intel Iris Plus Graphics 655 1536

[Freesurfer] error: Bad CPU type in executable WMH FreeSurfer

: Bad CPU type in executable" Is this machine too old to run WMH FreeSurfer? Best, Ian Johnson, B.A. Clinical Research Associate Division of Neurocritical Care & Emergency Neurology Yale School of Medicine E: ian.p.john...@yale.edu ___ Freesurfe

[Freesurfer] mri_WMHsynthseg error: Killed 9

posts that the "killed" error is because of an issue with RAM, but I have not run into this error in the past. The error occurs while on the "Pushing data through the CNN" step. There is no error message, terminal just prints &quo

[Freesurfer] ctx-lh-corpuscallosum

External Email - Use Caution Hi Freesurfers. There is a "ctx-lh/rh-corpuscallosum" label in Freesurfer, but the Corpus Callosum is not considered to be in the cortex.  Can you explain precisely what this label refers to? Th

Re: [Freesurfer] Recon-all 5.3.0 failing and I can't see the error message

rote: Not sure. Can you run this cd /execute/freesurfer2016/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i orig.mgz --o orig_nu.mgz and send the terminal output? On 6/29/2020 7:01 AM, Ian wrote: External Email - Use Caution I have attached the log

[Freesurfer] Recon-all 5.3.0 failing and I can't see the error message

External Email - Use Caution I have attached the log - is there any chance you could tell me what the problem is? Thanks, Ian -- Mon Jun 29 10:53:22 UTC 2020 /execute/freesurfer2016 /usr/local/freesurfer/bin/recon-all -all -subjid ./freesurfer2016 subjid freesurfer2016 setenv

[Freesurfer] Freesurfer 5.3.0 recon-all failure

/perl/5.28 /usr/share/perl/5.28 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/local/freesurfer/mni/bin/nu_correct line 37. BEGIN failed--compilation aborted at /usr/local/freesurfer/mni/bin/nu_correct line 37. Could you advise please? Thanks, Ian -- *Ian Hardi

Re: [Freesurfer] Ventricular location

he 3rd ventricle. > > I hope that is what you were asking? > > Tim > >> On June 17, 2020 at 11:41 AM Ian Hardingham wrote: >> >> >> External Email - Use Caution >> >> Are the ventricles currently in V6 Surf directory as a set of vertices, >

Re: [Freesurfer] Ventricular location

External Email - Use Caution Are the ventricles currently in V6 Surf directory as a set of vertices, or a labelled list of voxels, or anything like that? Ian On 16/06/2020 13:39, Ian wrote: External Email - Use Caution Hi Freesurfers. I'm looking to find the c

Re: [Freesurfer] Ventricular location

las N. Greve wrote: Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids On 6/16/2020 10:32 AM, Ian Hardingham wrote: External Email - Use Caution Is this only in FSL 7 Doug? I can't find it in 6. On 16/06/2020 14:59, Douglas N. Greve w

Re: [Freesurfer] Ventricular location

External Email - Use Caution Thank you so much Doug. Ian On 16/06/2020 15:44, Douglas N. Greve wrote: Yes, I put a linux version here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_segcentroids On 6/16/2020 10:32 AM, Ian Hardingham wrote: External Email - Use

Re: [Freesurfer] Ventricular location

External Email - Use Caution Is this only in FSL 7 Doug? I can't find it in 6. On 16/06/2020 14:59, Douglas N. Greve wrote: Try  mri_segcentroids. Run it with --help to get docs On 6/16/2020 8:39 AM, Ian wrote: External Email - Use Caution Hi Freesurfers.

[Freesurfer] Ventricular location

External Email - Use Caution Hi Freesurfers. I'm looking to find the center of the various Ventricles.  Are they included in the freesurfer segmentation images with a specific code? If not, what approach would you use? Thanks, Ian -- *Ian Hardi

Re: [Freesurfer] Get Freesurfer versions 4 and 5

External Email - Use Caution Sorry, found them, never mind! On 18/05/2020 12:26, Ian wrote: External Email - Use Caution Hi freesurfers, Is it possible to download freesurfer versions 4 and 5? Thanks, Ian -- *Ian Hardingham

[Freesurfer] Get Freesurfer versions 4 and 5

External Email - Use Caution Hi freesurfers, Is it possible to download freesurfer versions 4 and 5? Thanks, Ian -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu

Re: [Freesurfer] Which subject does recon-all register surfaces to?

External Email - Use Caution Thanks Bruce. On 13/05/2020 15:41, Bruce Fischl wrote: Hi Ian we don't register to an individual subject - we register to a probabilistic atlas compiled from many subjects. The fsaverage subjects were also generated from that data so they a

[Freesurfer] Which subject does recon-all register surfaces to?

BJECTS_DIR/fsaverage/lh.sphere.reg a registration to?  If not, where can I find the subject that recon-all registers to? Thanks, Ian -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailma

Re: [Freesurfer] Get Atlas surfaces in subject space

pace, not average space. So if I have five subjects - I would like the same number of points for each one, which I thought I would get by registering the average to each of them... On 11/05/2020 18:56, Douglas N. Greve wrote: Ian, it seems like you want two different things. When you run mri_sur

Re: [Freesurfer] Get Atlas surfaces in subject space

but it does not alter the number of vertices in them. There is no 1-to-1 correspondence between the vertices of the 2 meshes. May I ask why you need this? What do you want to achieve? Tim On May 11, 2020 at 2:11 PM Ian wrote: External Email - Use Caution I'm just going to try

Re: [Freesurfer] Get Atlas surfaces in subject space

External Email - Use Caution I'm just going to try this again, but this time with a different command: mris_apply_reg --src-xyz /usr/local/freesurfer/subjects/fsaverage/surf/lh.white --trg /home/ian/lh_reg.white --streg /usr/local/freesurfer/subjects/fsaverage

Re: [Freesurfer] Get Atlas surfaces in subject space

07/05/2020 22:45, Douglas N. Greve wrote: Isn't that what you got from the mri_surf2surf command? On 5/7/2020 3:08 PM, Ian Hardingham wrote: External Email - Use Caution Thanks Doug - yes, I'd like the vertex coordinates in the same format as the local subject surface file

Re: [Freesurfer] Get Atlas surfaces in subject space

es this mean an affine (12dof) transform? And what information do you want? An XYZ coordinate? On 5/7/2020 11:06 AM, Ian Hardingham wrote: External Email - Use Caution I'd like to get a set of points to compare across several brains, so that the nth point in brain A is in roughly t

Re: [Freesurfer] Get Atlas surfaces in subject space

ces) translated to positions on the target brain (which may well not be vertices in the target geometry.) On 07/05/2020 15:59, Douglas N. Greve wrote: I don't understand. What is the difference between the target brain and the target subject's vertices? On 5/7/2020 2:17

Re: [Freesurfer] Get Atlas surfaces in subject space

ces, which should be the number of vertices in the target subject (and is in the typical range for an individual subject) On 5/6/2020 10:21 AM, Ian Hardingham wrote: External Email - Use Caution FSLInfo attached, thanks Bruce. When trying to run freeview I get "freeview.bin: erro

Re: [Freesurfer] Get Atlas surfaces in subject space

00) c_(ras) : (-0.5431,  8.9290, -17.0723) file    : /media/ian/bronson/subject/T1_nifti.nii.gz Volume Geometry vox2ras -0.99905  -0.04362   0.0   92.25847; -0.04362   0.99905   0.0  -99.12585;  0.0   0.0   1.0  -145.07230;  0.0   0.0   0.0   1.0; Volume Geometry v

Re: [Freesurfer] Get Atlas surfaces in subject space

input_dir}/T1_nifti.nii.gz --trgsurfval {output_dir}/registered_lh.white My newly registered lh.white file is half the size: 3316997 May  6 10:41 /home/ian/cdm_registered_test/registered_lh.white (and appears to have half the vertices accordingly.) So this must be incorrect, or at least not my int

Re: [Freesurfer] Get Atlas surfaces in subject space

the same thing, but the interface might be a little easier On 5/5/2020 12:49 PM, Bruce Fischl wrote: no definitely not "w" format, which we don't use for anything anymore. YOu should use tval-xyz also I think On Tue, 5 May 2020, Ian Hardingham wrote: External Email

Re: [Freesurfer] Get Atlas surfaces in subject space

mi rh --srcsubject fsaverage --sval-xyz pial --trgsubject fs_target --trgsurfval ./registered_rh.pial --trg_type w The white calls output seems to be fine, but the pial ones aren't.  I somewhat naively trued trg_type pial but that wasn't correct. On 05/05/2020 17:33, Ian Hardingham wrote:

Re: [Freesurfer] Get Atlas surfaces in subject space

", but if it's ".pial" it outputs ".pial.w", which I find a little curious. Ian On 05/05/2020 16:34, Bruce Fischl wrote: yes, check out options like: --sval-xyz if you need further help though I'll have to defer to Doug :) Bruce On Tue, 5 May 2020, Ian

Re: [Freesurfer] Get Atlas surfaces in subject space

20 14:43, Bruce Fischl wrote: Hi Ian you can use mri_surf2surf to map surfaces between subjects, but our atlas isn't really a surface. You can use the surfaces in the fsaverage dir, but they are meant for visualization and are much smoother than individuals cheers Bruce On Tue, 5 May

[Freesurfer] Get Atlas surfaces in subject space

space. Any helpers on how to achieve this? Thanks, Ian -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] How is Total cortical gray matter volume calculated

value... or is the volume between the surfaces calculated somehow? Thanks, Ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] 8 Gb of ram

ainer image is based on Ubuntu; and nothing else is being explicitly run on the instance while recon-all is running. Thanks, Ian -- *Ian Hardingham* ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/ma

[Freesurfer] recon-all-failure with file links

ached the logs - the only immediate error I can see is "Cannot find rh.white.H". Any advice would be much appreciated, thank you. Ian -- *Ian Hardingham* Chief Technology Officer signature_873986710 ian.harding...@oxfordbraindiagnostics.com <mailto:terry.poll...@oxfordbraindiagnos

[Freesurfer] nu_correct: Command not found

i/bin:$PATH 2. I have set FREESURFER_HOME Attached at the end is some output from both failing and successful runs. 3. nu_correct exists in freesurfer/mni/bin 4. Perl is present and correct on both systems. Thank you in advance, Ian FAILING O

[Freesurfer] hippocampal subfield segmentation input mask?

like to try as input to see if it provides a better starting point than whole brain labels. Are there any other inputs we'd need? Best wishes, Ian Malone -- Research Associate Dementia Research Centre Queen Square Institute of Neurology

[Freesurfer] Nonisotropic PSF in mri_gtmpvc

Hello, Is there a way to specify a nonisotropic PSF when using mri_gtmpvc? I have reason to believe there are differences between the axial and transverse resolutions of the PET scanner in my study and would like to incorporate them if possible. Thanks, Ian Kennedy

[Freesurfer] generating new surface

I am looking for lies elsewhere. Any help would be highly appreciated!! ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only fo

[Freesurfer] public MRI dataset, alzheimer's and controls, MIRIAD

ase of this data was made possible through the support of the UK Alzheimer's Society and the kind permission of the original study participants and funders. Full acknowledgements can be found at <https://www.ucl.ac.uk/drc/research/miriad/Acknowledgements>. Best wishes for your future

[Freesurfer] Thresholding using FDR

values when nothing is significant? Thanks, Ian ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is

[Freesurfer] DODS Overlay

;s no intelligible way to make an overlay out of interactions, unless you look at the F-test output one contrast at a time (e.g., what areas show a significant interaction in thickness between dependents vs abusers and use in the last month?). Take care, Ian Ca

Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

Hi Thanks guys for the reply, I have fixed this now. ian > -Original Message- > From: dgw [mailto:dgwake...@gmail.com] > Sent: 07 March 2012 19:55 > To: Nick Schmansky > Cc: Ian Charest; freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] freesurfer 5.1 error:

Re: [Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

Hi again More on this note: Using the previous stable version 4.3.0 that I have installed here, I have absolutely no problem in running the same process. ian From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Ian Charest Sent: 07 March

[Freesurfer] freesurfer 5.1 error: MPR2MNI305_TARGET: Undefined variable

y orig.mgz in tkmedit and all seems fine. Any Idea what could be going wrong? Best Wishes Ian Charest == talairach_avi.log: /imaging/ic01/subjects/subject01/mri /imaging/local/software/freesurfer/5.1.0/i686//bin/talairach_avi --i orig.mgz --xfm transforms/talairach.auto.xfm $Id: talairach

Re: [Freesurfer] FreeSurfer & Ubuntu 11.10

de according to where your freesurfer install is and where your subject directory lies... alias freesurfer 'setenv FREESURFER_HOME /usr/local/freesurfer; setenv SUBJECTS_DIR ~/subjects; source $FREESURFER_HOME/SetUpFreeSurfer.csh' now if you close your terminal and open a new one, freesur

[Freesurfer] Probabilistic V1 labels to volume

I one should need a register.dat file here or even a template file, as I want to generate a volume in RAS space, from a label which I would think is also in RAS space. As for the template file, should it be orig.mgz? Any suggestions here would be appreciated!

Re: [Freesurfer] recommende pc and cuda

On 05/04/11 16:55, Richard G. Edgar wrote: > > On Tue, 2011-04-05 at 16:30 +0100, Ian Malone wrote: >> Richard G. Edgar wrote: >>> On the standard test case we use here, a full recon-all run takes 8 >>> hours on a 3.2 GHz Nehalem core, and about 4 hours 20 mins

Re: [Freesurfer] recommende pc and cuda

Richard G. Edgar wrote: On Tue, 2011-04-05 at 11:23 +0200, Knut J Bjuland wrote: Will a Tesla C2050 or another good CPU be able to reduce the running time from 20-24 hr to less time like for instance 8hr or below that time. On the standard test case we use here, a full recon-all run ta

[Freesurfer] labels and transforming them

things that might be going wrong here or other strategies to try? Also, assuming I get the transformation right, will adjusting the label point volume to match the new voxel dimensions make any difference if the the threshold is set at zero? Thanks, Ian __

Re: [Freesurfer] mri_convert failure

The file is the right size, however further investigation shows that vox_offset in the .hdr file was (incorrectly) non-zero; equal to 1, so mri_convert is correct in skipping one byte at the start. Sorry for the fuss. Ian Douglas N Greve wrote: Can you verify that the file is the right

[Freesurfer] mri_convert failure

e-pub-v4.0.3 Kernel info: Linux 2.6.21.5-smp i686 Thanks, Ian Malone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] mri_label2vol aliasing problem

acent ones). Using the 1mm^3 voxel registered volume as the template does not show this problem, neither does viewing the label overlaid on orig.mgz in tkmedit. Is there anything I can adjust to avoid this while still outputting a volume in the original image dimensions? Thanks, Ian M

Re: [Freesurfer] Image deidentification

There is also nifti_tool which comes with nitfilib (nifticlib) http://sourceforge.net/project/showfiles.php?group_id=126549 $ nifti_tool -disp_hdr -infiles mynifti.nii imalone Doug Greve wrote: nifti generally does not have the capability to save patient info. I might if the software that cre

Re: [Freesurfer] mri_watershed regions appearing round edge, freesurfer 4.0.2

It's not terrible; it can be worked around. But it does feel more like a bug than a feature, as these voxels are un-connected with any in the brain. It looks a bit like the edge of a bounding box. Thanks, Ian Bruce Fischl wrote: Hi Ian, mri_watershed minimizes a risk functional in whi

[Freesurfer] mri_watershed regions appearing round edge, freesurfer 4.0.2

for your time, Ian Malone ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer