[Freesurfer] mri_volsynth fails but exits with 0 exit status

[Aaron Tanenbaum]

External Email - Use Caution

I am currently running FreeSurfer 7.4.  I wrote a script using the program
mri_volsynth.  I noticed for the first time the program was trying to write
files where it did not have write permissions. It outputted a few error
messages but gave a 0 exit status. It would be nice to have it exit with a
nonzero exit status.
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Re: [Freesurfer] ERROR: flag i unrecognized

[Aaron Tanenbaum]

External Email - Use Caution

I noticed the "-" used for the i and all is longer than the one used  for
the s.  It's a subtle difference and a problem if you are copying text from
Windows to Linux. Just replace the long hyphen with the short one.

On Sat, Apr 15, 2023 at 7:02 PM Francisco Polito haro 
wrote:

> External Email - Use Caution
>
>
> I'm trying to start a scan but I can't get it to start the recon process
> there, I get an error, I don't know what I'm doing wrong. with the test
> subject of BERT that marks the tutorial if it does, but with my file it
> doesn't, I attach the message and screenshot of the error that appears to
> me:
>
>
>
>
>
> Sin mas por el momento, reiterando mi subordinación y respeto, reciba un
> caluroso saludo.
>
>
> Sufragio Efectivo, No Reelección
> LFA Francisco Polito Haro
> CP 12915210
>
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>  .
>
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[Freesurfer] recommended change to FreeSurferEnv.sh

[Aaron Tanenbaum]

External Email - Use Caution

Recently FSL has changed the location of the bin directory they want you to
use.

The FreeSurfer setup script adds the old binary folder to the PATH not the
new one.  This is causing quite a bit of trouble for me. I made changes to
the FreeSurferEnv.sh. I removed lines  440-446 and in its place I put the
following. The echo line probably needs to be changed but it works.

if [ -d $FSL_DIR/share/fsl/bin ]; then
> export FSL_BIN=$FSL_DIR/share/fsl/bin
> elif [ -d $FSL_DIR/bin ]; then
> export FSL_BIN=$FSL_DIR/bin
> else
> if [[ $output == 1 ]]; then
> echo "WARNING: $FSL_BIN does not exist.";
> fi
> fi
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[Freesurfer] head in a bad position in scanner

[Aaron Tanenbaum]

External Email - Use Caution

We acquired some data this morning where the participant's head was in an
unusual orientation. The participant has cervical dystonia. I have
processed data like this before and freesurfer always fails. I am assuming
Freesurfer is unable to register the image.  I have not even run this image
through freesurfer yet. Is there a way to deal with this without altering
the image?
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Re: [Freesurfer] Substantia nigra segmentation status

[Aaron Tanenbaum]

External Email - Use Caution

Good luck. It requires a 7T to separate the compacta and reticulata.
Localizing the the substantia nigra  is impossible with standard MPRAGES
but can be done if you modify the sequence or use a adequate T2 .   There
are papers that discuss how to localize it you do not need FreeSurfer.

On Mon, Mar 6, 2023 at 4:57 PM Christian Owen  wrote:

> External Email - Use Caution
>
> Hi,
>
> The latest post I could find about substantia nigra segmentation in
> FreeSurfer is from May 2020
> .
> As of that post, it was not possible. Is it still not possible? If that's
> the case:
>
> - is substantia nigra segmentation on the roadmap?
> - is there anything a software engineer could do to help make it happen? I
> cannot promise any resources atm, but there's a chance we could help out
> (if it turns out to be enough of a priority).
>
> Best,
> Christian
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>  .
>
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Re: [Freesurfer] Apply a nonlinear transform to a surface.

[Aaron Tanenbaum]

External Email - Use Caution

I think that only works for gifti files. I need it in freesurfer
coordinates. Thank you for responding.

On Fri, Mar 3, 2023, 7:30 PM Glasser, Matt  wrote:

> External Email - Use Caution
>
> You can do this with wb_command.  Dunno if FreeSurfer offers this.
>
>
>
> Matt.
>
>
>
> *From: * on behalf of Aaron
> Tanenbaum 
> *Reply-To: *Freesurfer support list 
> *Date: *Friday, March 3, 2023 at 7:26 PM
> *To: *Freesurfer 
> *Subject: *[Freesurfer] Apply a nonlinear transform to a surface.
>
>
>
> *External Email - Use Caution*
>
> I am working on a project that will involve applying nonlinear work to a
> freesurfer surface.   This project is in its infancy. I have not figured
> out all the details.  The nonlinear transform will be in either FNIRT or
> ANTS format. Does anyone know how to do this?
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
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>  .
>
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[Freesurfer] Apply a nonlinear transform to a surface.

[Aaron Tanenbaum]

External Email - Use Caution

I am working on a project that will involve applying nonlinear work to a
freesurfer surface.   This project is in its infancy. I have not figured
out all the details.  The nonlinear transform will be in either FNIRT or
ANTS format. Does anyone know how to do this?
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Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic segmentation

[Aaron Tanenbaum]

External Email - Use Caution

Hi,
I saw this thread and was wondering about the details of this patch. Does
this patch affect the standard recon-all call or is this meant for a
special flag. Also I was also wondering what issue did it solve?
Thank you.

On Wed, Feb 22, 2023 at 11:52 PM Kumar, Avnish 
wrote:

> Hi Katie,
>
> The core.py file has been updated now. Please try downloading it again and
> applying the same fix
> 
> as before.
>
> Best,
> Avnish
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson <
> katie.job...@temple.edu>
> *Sent:* Monday, February 6, 2023 3:17 PM
> *To:* Freesurfer support list 
> *Subject:* Re: [Freesurfer] [External] Re: 7.3.2-patch issues - thalamic
> segmentation
>
>
> External Email - Use Caution
>
> Hi FS experts,
>
> Apologies for my late follow up.
>
> In reference to the previous conversation, I added the core.py file to the
> correct subdirectory to complete the thalamic nuclei segmentation. I
> received an error still, albeit a different error:
>
> Traceback (most recent call last):
>
>   File "/usr/local/freesurfer-7.3.2/python/scripts/segment_subregions",
> line 6, in 
>
> from freesurfer import subregions
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/__init__.py",
> line 1, in 
>
> from freesurfer.subregions.process import structure_names
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/process.py",
> line 8, in 
>
> from freesurfer.subregions.thalamus import ThalamicNuclei
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/thalamus.py",
> line 9, in 
>
> from freesurfer.subregions.core import MeshModel
>
>   File
> "/usr/local/freesurfer-7.3.2/python/packages/freesurfer/subregions/core.py",
> line 9, in 
>
> from gems.subregions import utils
>
> ImportError: cannot import name 'utils' from 'gems.subregions' (unknown
> location)
>
> I am assuming this is because the core.py script was previously housed in
> the '/gems/subregions' subdirectory, and is attempting to import 'utils'
> from there. Is there any way to edit this file (core.py) to call on this
> 'utils' function?
>
> Please let me know if I can clarify my question in any way and thank you
> in advance for your help!
>
> Best Wishes,
> Katie
> --
> Katie Jobson, M.S. | Personal Website
> 
> Ph.D. Student | Cognitive Neuroscience Lab
> 
> Department of Psychology and Neuroscience | Temple University
>
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Kumar, Avnish <
> avnish.ku...@mgh.harvard.edu>
> *Sent:* Thursday, December 8, 2022 10:19 AM
> *To:* Freesurfer support list 
> *Subject:* [External] Re: [Freesurfer] 7.3.2-patch issues - thalamic
> segmentation
>
> Hi Katie,
>
> Thank you for pointing this out! Yes, please make changes to the core.py
> script in your '$FREESURFER/python/packages/freesurfer/subregions/'
> folder. I will update the patch instructions to reflect this as well.
>
> Best,
> Avnish
> --
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Katie Rose Jobson <
> katie.job...@temple.edu>
> *Sent:* Wednesday, December 7, 2022 3:35 PM
> *To:* freesurfer@nmr.mgh.harvard.edu 
> *Subject:* [Freesurfer] 7.3.2-patch issues - thalamic segmentation
>
>
> External Email - Use Caution
>
> Hi FS experts,
>
> I am attempting to implement the patch on version 7.3.2 for issues with
> thalamic segmentation. I followed the instructions found 

[Freesurfer] neurological view on command line

[Aaron Tanenbaum]

External Email - Use Caution

Is there a flag on the command line to turn on neurological view or do I
have to turn it on in the GUI.
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[Freesurfer] Senior research position

[Aaron Tanenbaum]

External Email - Use Caution

Please see attached for a Senior research position job description.

Please apply for the position at 
https://secure-web.cisco.com/1u02-AJuClQt7sTxQ63p9YV9P4EzHp2M0YbFhpmhtEnqyD16PUdBlzpsFIb6u54dz_L5fagYqxf_NJurrNhuGudmHEk16l87Pd3QdoRWvU-yoEkJ400Valgkv7doBEAjCvK-tCIFuDC1j4KOjT7w8sWRZDUl1hFG_38fGH7JdJctYHssIuStlUXFSIygRA0gYr6KJEtbIS5Dos_B-Tky5gAbsuoIyRYEioGz0V-gpYhqQI92mgtqZqYmm2U0VhItKR_bcW7gVmfX1Mz5dhJBKGicSV0BXrlUfNz5qATE0-7d5zsNAL5ac2A7HgQi4Rxox0_ubR9bK6W6EWha6zxqSCw/https%3A%2F%2Fjobs.wustl.edu%2F
 Do not apply for
the position over email, email will be ignored.



Aaron Tanenbaum


Senior Neuroimaging Engineer,ReqJR72355.docx
Description: MS-Word 2007 document
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Re: [Freesurfer] High resolution T1

[Aaron Tanenbaum]

External Email - Use Caution

On Mon, Jan 30, 2023 at 12:40 PM Lee, Sang Hoon 
wrote:

> External Email - Use Caution
>
> Dear, Matt,
>
>
>
> What kind of issues did you have with version 7.x and the hires stream?
>
> It would help us to know what we are facing…
>
> Thanks.
>
>
>
> Sang
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Glasser, Matt
> *Sent:* Monday, January 30, 2023 1:23 PM
> *To:* Freesurfer support list 
> *Subject:* [EXTERNAL] Re: [Freesurfer] High resolution T1
>
>
>
> *CAUTION:* This email originated from outside the organization. *DO NOT
> CLICK ON LINKS* *or* *OPEN ATTACHMENTS* unless you know and trust the
> sender.
>
> *External Email - Use Caution*
>
> We showed improved data (more accurate surface placement leading to more
> accurate myelin maps) in prior publications (Glasser et al., 2013; 2014
> Neuroimage).  It makes a difference for cortical thickness too (e.g.,
> falsely too low cortical thickness in auditory cortex in Glasser and Van
> Essen 2011 Journal of Neuroscience).  That said, at least in our hands we
> have had some issues with FreeSurfer 7.X and the hires stream.  I’ve been
> hoping that the FS folks have a chance to investigate that soon, but for
> now we have stuck with FS 6.0 for the HCP and HCP Pipelines.
>
>
>
> In general, it’s good to have at least two voxels of grey matter for even
> the thinnest cortical areas (e.g., somatosensory area 3b, visual area V1),
> which are about 1.6mm thick.  This is where the HCP’s recommendation of at
> least 0.8mm isotropic T1w and T2w or FLAIR images comes from (and why we
> didn’t stick with the typical 1mm resolution recommendation that was
> prevalent before the HCP).
>
>
>
> Matt.
>
>
>
> *From: * on behalf of "Lee, Sang
> Hoon" 
> *Reply-To: *Freesurfer support list 
> *Date: *Monday, January 30, 2023 at 9:22 AM
> *To: *"freesurfer@nmr.mgh.harvard.edu" 
> *Subject: *[Freesurfer] High resolution T1
>
>
>
> *External Email - Use Caution*
>
> I understand that from Version 7.0, better high resolution surface
> reconstruction with -hires is done.
>
> My question is, if we use higher resolution T1, such as 0.8mm, will it
> improve the accuracy of the cortical thickness measurement?  If yes, is
> there any reference?
>
> Thank you so much for your time!
>
>
>
>
>
> *Sang H. Lee* (Sr. Research Associate III)
>
> UM-Millier School of Medicine
>
>
>
>
>
>
> --
>
> The materials in this message are private and may contain Protected
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[Freesurfer] FSL on recon-all

[Aaron Tanenbaum]

External Email - Use Caution

Hello FreeSurfers,
I just need to know if the FSL is used in the recon-all scripts. Basically
if FSL_DIR is different will the recon-all produce different values.
Thank you
Aaron.
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Re: [Freesurfer] mri_mask error exits returns a zero exit status

[Aaron Tanenbaum]

External Email - Use Caution

I should have said I am using FS 7.3 on Ubuntu 20.04

On Tue, Jan 10, 2023 at 12:23 PM Aaron Tanenbaum <
aaron.b.tanenb...@gmail.com> wrote:

> Hello,
> FYI, I recently noticed that mri_mask returns a zero exit status when it
> is unable to write the output.
>
>
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[Freesurfer] mri_mask error exits returns a zero exit status

[Aaron Tanenbaum]

External Email - Use Caution

Hello,
FYI, I recently noticed that mri_mask returns a zero exit status when it is
unable to write the output.
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[Freesurfer] freeview: set file as read only

[Aaron Tanenbaum]

External Email - Use Caution

Hello,
Is there a way to set a loaded volume as read only in freeview on the
command line?
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[Freesurfer] create a mgz with one value

[Aaron Tanenbaum]

External Email - Use Caution

Hello,
I am trying to generate a mgz with identical header and dimensions as
another mgz file. However I would like all voxels to be set to one value.
What is the best way to do this?

Thank you
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[Freesurfer] Change made in the release of FSL 6.0.6 may affect Freesurfer

[Aaron Tanenbaum]

External Email - Use Caution

I have noticed a change made in the release of FSL 6.0.6  that may affect
FreeSurfer. FSL executables now lie in ${FSLDIR}/share/fsl/bin not
${FSLDIR}/bin. The Freesurfer set up script adds ${FSLDIR}/bin to the PATH.
Not sure if this causes any trouble.
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[Freesurfer] FreeView feature request

[Aaron Tanenbaum]

External Email - Use Caution

I am looking set up freesurfer to do two things. If they are not currently
possible then I would like to  submit two feature requests for freeview.
Here they are

When making voxel edits, it would be useful to see all voxels the mouse is
pointing to. Currently the mouse looks like a pen pointing to one voxel. If
my brush size is 5, it would be nice if all 25 voxels are highlighted.

It would also be convenient to have the voxels that have been edited in a
single brush stroke highlighted.. Frequently I will be making an edit to an
image while another image is overlaid on top of it. So I can not see my
edits. forcing me to toggle between images.

Thank you
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[Freesurfer] Operating systems

[Aaron Tanenbaum]

External Email - Use Caution

Hi FS development team,
We are about to install an OS on one of our servers. We are trying to
figure out what OS to use.  I see that FS 7.3 now is compiled for Ubuntu
20.0. Which is great. Will you mainly be supporting just Ubuntu in the
future. Most supercomputers run Redhat which worked great when you compiled
with CentOS. I was wondering if you are going to consider either rocky or
almalinux. Both are distributions that came out of the ashes of centos
which is why I ask.
Aaron Tanenbaum
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Re: [Freesurfer] aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved

[Aaron Tanenbaum]

External Email - Use Caution

Correction, not cerebellum inclusions but dural inclusion being labeled as
cerebellum. When editing I am setting these dural inclusion as 0 in the
brainmask, i am using -autorecon2 flag, and I never edit more then one
image before rerunning recon-all.

On Wed, Jun 22, 2022, 9:23 AM Aaron Tanenbaum 
wrote:

> So I believe I posted something like this a while ago. My observation is
> that edits removing voxel from the brain mask does not always remove
> inclusions for the cerebellum. It seem to work for the rest of the brain.
> I find this to be a common occurrence.
>
> On Thu, Jun 16, 2022, 7:02 PM Keefe, Sarah  wrote:
>
>> External Email - Use Caution
>>
>> Hi FreeSurfer Team,
>>
>> Our group is in the process of switching to Freesurfer 7.1.1 from 5.3. We
>> have been taking advantage of Freesurfer 7's aseg.presurf volume to add in
>> correction of unlabeled cerebellum to our standard edit checklist rather
>> than our previous workflow of having a Freesurfer fail our quality control
>> standards and be excluded from analysis if too much cerebellum is unlabeled
>> on aparc+aseg segmentation. We're consistently running into an issue when
>> we have a Freesurfer that requires corrections to both brainmask.mgz and
>> aseg.presurf.mgz.
>>
>> An example of when this happens is if the Freesurfer output labels dura
>> as cerebellum cortex on aparc+aseg (which requires erasing the included
>> dura from brainmask.mgz) and the output also has an exclusion of cerebellum
>> from the aparc+aseg segmentation (which requires correctly labeling the
>> excluded voxels on aseg.presurf.mgz). We have found that if we edit both
>> the aseg.presurf.mgz and brainmask.mgz volumes and then rerun recon-all
>> with both, the cerebellum exclusion segmentation fix does not "take"
>> completely and individual voxels in the cerebellum that were corrected in
>> the edited volume are still left unlabeled. We have 100% confirmed that our
>> labeling edits to aseg.presurf are correct and complete before this
>> happens. To reduce confusion and attempt some consistency across our
>> editing team, we relaunch recon-all with the same flags every time:
>> -autorecon2 -autorecon3 -qcache
>>
>> To work around this issue, we implemented a workflow where editors will
>> make brainmask.mgz corrections, then rerun recon-all (rerun 1), and then
>> make aseg.presurf corrections, and rerun recon-all again (rerun 2). This
>> seems to work although it is frustrating since we are trying to minimize
>> the number of reruns of recon-all and we typically tell people to stop and
>> make a final quality control decision after 3 reruns.
>>
>> What we are finding is if another issue pops up on brainmask.mgz after
>> rerun 2 that then needs corrections (e.g. other areas of dura are
>> incorrectly included in the pial surface or aparc+aseg cerebellum labeling
>> but weren't included before so weren't erased) then after making those
>> edits and rerunning recon-all, the previously corrected aparc+aseg
>> cerebellum segmentation shows "missing" unlabeled voxels, same as if we had
>> run recon-all once with both aseg.presurf and brainmask volumes edited.
>>
>> The attached image shows an example of our process and the issues we're
>> seeing. The end result (F) also happens if we edit both brainmask.mgz and
>> aseg.presurf.mgz edits and rerun recon-all once with both included.
>>
>> screenshot A is the aparc+aseg.mgz of the original recon-all output (run
>> 0) where cerebellum is unlabeled (red arrows). There is also visible dura
>> labeled as cerebellum that we need to fix (yellow arrow).
>>
>> screenshot B is the aparc+aseg.mgz of the recon-all rerun output after
>> just the brainmask.mgz was edited and saved (run 1). Additional
>> segmentation issues have appeared in addition to the original ones (red
>> arrows). This screenshot also shows an example of the type of edit we are
>> doing to brainmask - we have erased dura from brainmask.mgz to correct the
>> cerebellum cortex labeling and the edit worked (yellow arrow).
>>
>> screenshot C is the aseg.presurf.mgz volume after run 1 before editing
>> for the cerebellum exclusion issue.
>>
>> screenshot D is our edited and saved aseg.presurf volume BEFORE we run
>> the second recon-all relaunch. We have corrected the labeling (green
>> arrows).
>>
>> screenshot E is the aparc+aseg.mgz after a recon-all relaunch with only
>> the new edit to aseg.presurf. (run 2). The cerebellum exclusion error has
>> been fixed in aparc+aseg

Re: [Freesurfer] aseg.presurf edits are undone or incomplete when brainmask.mgz edits are involved

[Aaron Tanenbaum]

External Email - Use Caution

So I believe I posted something like this a while ago. My observation is
that edits removing voxel from the brain mask does not always remove
inclusions for the cerebellum. It seem to work for the rest of the brain.
I find this to be a common occurrence.

On Thu, Jun 16, 2022, 7:02 PM Keefe, Sarah  wrote:

> External Email - Use Caution
>
> Hi FreeSurfer Team,
>
> Our group is in the process of switching to Freesurfer 7.1.1 from 5.3. We
> have been taking advantage of Freesurfer 7's aseg.presurf volume to add in
> correction of unlabeled cerebellum to our standard edit checklist rather
> than our previous workflow of having a Freesurfer fail our quality control
> standards and be excluded from analysis if too much cerebellum is unlabeled
> on aparc+aseg segmentation. We're consistently running into an issue when
> we have a Freesurfer that requires corrections to both brainmask.mgz and
> aseg.presurf.mgz.
>
> An example of when this happens is if the Freesurfer output labels dura as
> cerebellum cortex on aparc+aseg (which requires erasing the included dura
> from brainmask.mgz) and the output also has an exclusion of cerebellum from
> the aparc+aseg segmentation (which requires correctly labeling the excluded
> voxels on aseg.presurf.mgz). We have found that if we edit both the
> aseg.presurf.mgz and brainmask.mgz volumes and then rerun recon-all with
> both, the cerebellum exclusion segmentation fix does not "take" completely
> and individual voxels in the cerebellum that were corrected in the edited
> volume are still left unlabeled. We have 100% confirmed that our labeling
> edits to aseg.presurf are correct and complete before this happens. To
> reduce confusion and attempt some consistency across our editing team, we
> relaunch recon-all with the same flags every time: -autorecon2 -autorecon3
> -qcache
>
> To work around this issue, we implemented a workflow where editors will
> make brainmask.mgz corrections, then rerun recon-all (rerun 1), and then
> make aseg.presurf corrections, and rerun recon-all again (rerun 2). This
> seems to work although it is frustrating since we are trying to minimize
> the number of reruns of recon-all and we typically tell people to stop and
> make a final quality control decision after 3 reruns.
>
> What we are finding is if another issue pops up on brainmask.mgz after
> rerun 2 that then needs corrections (e.g. other areas of dura are
> incorrectly included in the pial surface or aparc+aseg cerebellum labeling
> but weren't included before so weren't erased) then after making those
> edits and rerunning recon-all, the previously corrected aparc+aseg
> cerebellum segmentation shows "missing" unlabeled voxels, same as if we had
> run recon-all once with both aseg.presurf and brainmask volumes edited.
>
> The attached image shows an example of our process and the issues we're
> seeing. The end result (F) also happens if we edit both brainmask.mgz and
> aseg.presurf.mgz edits and rerun recon-all once with both included.
>
> screenshot A is the aparc+aseg.mgz of the original recon-all output (run
> 0) where cerebellum is unlabeled (red arrows). There is also visible dura
> labeled as cerebellum that we need to fix (yellow arrow).
>
> screenshot B is the aparc+aseg.mgz of the recon-all rerun output after
> just the brainmask.mgz was edited and saved (run 1). Additional
> segmentation issues have appeared in addition to the original ones (red
> arrows). This screenshot also shows an example of the type of edit we are
> doing to brainmask - we have erased dura from brainmask.mgz to correct the
> cerebellum cortex labeling and the edit worked (yellow arrow).
>
> screenshot C is the aseg.presurf.mgz volume after run 1 before editing for
> the cerebellum exclusion issue.
>
> screenshot D is our edited and saved aseg.presurf volume BEFORE we run the
> second recon-all relaunch. We have corrected the labeling (green arrows).
>
> screenshot E is the aparc+aseg.mgz after a recon-all relaunch with only
> the new edit to aseg.presurf. (run 2). The cerebellum exclusion error has
> been fixed in aparc+aseg (green arrows). This run 2 of recon-all caused
> more issues to show up that required more brainmask.mgz edits.
>
> screenshot F is what we see if we edit brainmask.mgz again and rerun
> recon-all (run 3). The output of run 3 shows missing voxels in the
> cerebellum where we had fixed them before. Unlabeled voxels appear
> throughout the areas that were edited in C and were corrected in D.
>
> We try to minimize edits and maintain consistency across our editing team
> by asking people to only erase dura from brainmask.mgz that has been
> erroneously included in the cerebellum labelling or in the pial surface
> (rather than other dura that also happens to be included in the
> brainmask.mgz). We also ask people to relaunch recon-all with the same
> -autorecon2 -autorecon3 -qcache flags each time for consistency across our
> data. 

Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

[Aaron Tanenbaum]

External Email - Use Caution

Are there special flags. There are differences between autorecon1 for both
pipeline. Does 7.2 update some of the files like for instance the T1.mgz do
to differences in the normalizations.

On Sun, Jun 19, 2022, 3:55 PM Douglas N. Greve 
wrote:

> You should be able to run 7.2 on top of the 5.3 and at will take all your
> edits (make a copy of your 5.3 data first:)
>
>
> On 6/14/2022 5:26 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
> to do.  I see that you can give freesurfer a brainmask. I was thinking of
> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
> wise idea? Do you have any objections?
>
> ___
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Re: [Freesurfer] using brain mask from older FreeSurfer version on a newer

[Aaron Tanenbaum]

External Email - Use Caution

Great. glad I was of some help. I still need my questions answered.

On Tue, Jun 14, 2022 at 4:33 PM Bouchra Guelib <
bouchra.gue...@univ-constantine2.dz> wrote:

> External Email - Use Caution
>
> The problem is solved, I just changed the freesurfer version , thnx for
> your help
>
> Le mar. 14 juin 2022 à 22:27, Aaron Tanenbaum 
> a écrit :
>
>> External Email - Use Caution
>>
>> Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans
>> to do.  I see that you can give freesurfer a brainmask. I was thinking of
>> giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
>> wise idea? Do you have any objections?
>> ___
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[Freesurfer] using brain mask from older FreeSurfer version on a newer

[Aaron Tanenbaum]

External Email - Use Caution

Our lab is moving from FreeSurfer 5.3 to 7.2. We have thousands of scans to
do.  I see that you can give freesurfer a brainmask. I was thinking of
giving freesurfer a brainmask from the previous from 5.3 to 7.1. Is this a
wise idea? Do you have any objections?
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Re: [Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

[Aaron Tanenbaum]

External Email - Use Caution

What about for 7.1?

On Fri, Oct 1, 2021 at 10:23 AM Douglas N. Greve 
wrote:

> What version are you running? In 7.2, it will automatically set the t2pial
> flag when you specify -t2
>
> On 9/27/2021 11:53 AM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
> What does Freesurfer do with a T2 if you do not use the t2pial flag?
>
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[Freesurfer] What does Freesurfer do with a T2 if you do not use the t2pial flag

[Aaron Tanenbaum]

External Email - Use Caution

What does Freesurfer do with a T2 if you do not use the t2pial flag?
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Re: [Freesurfer] Announcing FreeSurfer version 7.2

[Aaron Tanenbaum]

External Email - Use Caution

Read the release notes.  Can I with the new version run a recon-all over
processed 7.1.1.  I am interested in the ability to edit filled.mgz and
applying this to 7.1.1 recons.

On Mon, Jul 19, 2021 at 5:46 PM Douglas N. Greve 
wrote:

> We are  please to announce version 7.2. Mostly bug fixes and
> behind-the-scenes enhancements. But there are a few new goodies and one
> new "known issue" about defacing. Check out
> https://secure-web.cisco.com/1ncOzuZ5zSOChH82g2B5B18lsyS_oEgAlsOqNBwjRBfOX6dfCND4jEsGCslQiItXGhoadIOuNCP9Gdmotj05UDElZXc90oNGCyvZru1po1g8cNxA7SoCM43_jzv-wXfMs5Tj0EkP6TSPvm7uUDBsbHfFfclxf04AiFYRNhml_unsZDdggeQmLirCZ8UYNmHtG1ZHmG-PJVrMZpkjwzAtOS6RxZWBbuUaph-jzKfnDTTvy8xrvDR2st2Ue34xIf3G24-lzCJ1yyH-YVAjKWSfFqA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FReleaseNotes
> doug
>
>
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[Freesurfer] The lookuptable value of Virchow–Robin space

[Aaron Tanenbaum]

External Email - Use Caution

Ideally, what should Virchow–Robin space be labeled as.
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Re: [Freesurfer] Question about a feature introduced in FS 7.0 {Disarmed}

[Aaron Tanenbaum]

External Email - Use Caution

Thank you for responding. So before you responded, I tried a few things
out. one of them was to make the edit to the image and then run recon-all
with "-autorecon2-noaseg -autorecon3". I found this to move the surface
however the aparc+aseg file had the voxel I altered as 247. Last night I
tried what you suggest with the same alterations to the aseg.presurf file,
I found the surface and aparc+aseg was unchanged.

On Wed, Dec 23, 2020 at 12:28 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> I don't have any example, but the idea is pretty simple. If you want to
> freeze a point on the surface, open aseg.presurf.mgz and the surfaces for
> your subject, eg,
> tkmeditfv subject nu.mgz -seg aseg.presurf.mgz -surfs
> Then edit the aseg.presurf.mgz to change the voxels where you want to
> freeze to value 247 (FreezeSurface in
> $FREESURFER_HOME/FreeSurferColorLUT.txt)
> Then run recon-all with -autorecon2-surfonly -autorecon3
>
>
> On 12/22/2020 12:08 PM, Aaron Tanenbaum wrote:
>
> External Email - Use Caution
> So I never got a response for my question. At least can someone tell me
> the recon-all flags needed after editing the aseg.presurf.mgz file.  I am
> also assuming that this feature is also available for 7.1.1.
>
> On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum <
> aaron.b.tanenb...@gmail.com> wrote:
>
>> I am curious about a feature introduced in FS 7.0  In the release notes
>> it says, "Ability to freeze the surface at points labeled 247 in the
>> aseg.presurf.mgz" I was interested to know what this feature can do. Do you
>> have any examples of when this should be used?
>>
>> Aaron Tanenbaum
>>
>
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Re: [Freesurfer] Question about a feature introduced in FS 7.0

[Aaron Tanenbaum]

External Email - Use Caution

So I never got a response for my question. At least can someone tell me the
recon-all flags needed after editing the aseg.presurf.mgz file.  I am also
assuming that this feature is also available for 7.1.1.

On Wed, Dec 16, 2020 at 10:27 AM Aaron Tanenbaum <
aaron.b.tanenb...@gmail.com> wrote:

> I am curious about a feature introduced in FS 7.0  In the release notes it
> says, "Ability to freeze the surface at points labeled 247 in the
> aseg.presurf.mgz" I was interested to know what this feature can do. Do you
> have any examples of when this should be used?
>
> Aaron Tanenbaum
>
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[Freesurfer] Question about a feature introduced in FS 7.0

[Aaron Tanenbaum]

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I am curious about a feature introduced in FS 7.0  In the release notes it
says, "Ability to freeze the surface at points labeled 247 in the
aseg.presurf.mgz" I was interested to know what this feature can do. Do you
have any examples of when this should be used?

Aaron Tanenbaum
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[Freesurfer] Compiling freesurfer 6.0 on centos 8.1

[Aaron Tanenbaum]

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Hello All,
I was wondering have any of you compiled FreeSurfer 6.0 on centos 8.1. And
if so, have you had problem with it. Our lab got a new server, we are
contemplating which operating system we should install. So I am going
through the software to see what works and what does not on different
versions of centos.
Aaron Tanenbaum
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[Freesurfer] freesurfer 6.0 hires fix

[Aaron Tanenbaum]

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I noticed that you guys released a fix to improve the -hires option.  I
have been processing some of our data using the hires flag. if i use this
fix do i need to run recon-all from the beginning or can I run over the old
folders?
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Re: [Freesurfer] multiple T2s

[Aaron Tanenbaum]

External Email - Use Caution

Thank you dude

On Sun, Sep 8, 2019 at 9:22 AM Bruce Fischl 
wrote:

> Hi Aaron
>
> you may need to motion correct and average them yourself. We'll put it on
> our feature request list though
>
> cheers
> Bruce
> On Sat, 7 Sep 2019, Aaron Tanenbaum wrote:
>
> >
> > External Email - Use Caution
> >
> > Does freesurfer 6.0 have the ability to use multiple T2s in recon-all.
> If so
> > how does one get it to work. It only seems to use the last T2 in the
> call to
> > recon-all.
> >
> >
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[Freesurfer] multiple T2s

[Aaron Tanenbaum]

External Email - Use Caution

Does freesurfer 6.0 have the ability to use multiple T2s in recon-all. If
so how does one get it to work. It only seems to use the last T2 in the
call to recon-all.
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Re: [Freesurfer] T2 seq. for hippocampus ??

[Aaron Tanenbaum]

External Email - Use Caution

Sorry sent that last email by accident. Here is the finished version

Eugenio,
You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but
the Flair is.  Is a FLAIR in general not beneficial. Can you please
elaborate.

On Tue, Jun 25, 2019 at 2:20 PM Aaron Tanenbaum 
wrote:

> Eugenio,
> You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but
> the Flair is.  Is a FLAIR in general not benifisiol
>
> On Fri, May 18, 2018 at 2:02 PM Anik Dar  wrote:
>
>> External Email - Use Caution
>>
>> Hi All,
>>
>> I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1
>> cubic mm MPRAGE. Can you please let me know whether I should use only T1
>> or should I use one of the additional seq. for hippocampal subfield
>> segmentation ?
>>
>> cheers
>>
>> Nik
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>> addressed. If you believe this e-mail was sent to you in error and the
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>> HelpLine at
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Re: [Freesurfer] T2 seq. for hippocampus ??

[Aaron Tanenbaum]

External Email - Use Caution

Eugenio,
You said the T1+T2 would be best. The T2 Nik has is not 1mm isotropic but
the Flair is.  Is a FLAIR in general not benifisiol

On Fri, May 18, 2018 at 2:02 PM Anik Dar  wrote:

> External Email - Use Caution
>
> Hi All,
>
> I have 1x1x3 cubic mm T2 and 1x1x1 cubic mm FLAIR, in addition to 1x1x1
> cubic mm MPRAGE. Can you please let me know whether I should use only T1
> or should I use one of the additional seq. for hippocampal subfield
> segmentation ?
>
> cheers
>
> Nik
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>
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[Freesurfer] How do I get FreeSurfer to use a custom Talairach target.

[Aaron Tanenbaum]

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I am wondering if there is any documentation about getting FreeSurfer to
use a custom Talairach target.
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[Freesurfer] Recon-all taking 20 hours to run.

[Aaron Tanenbaum]

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I ran 38 subjects through Freesurfer 6.0 on a supercomputer here at Washu.
The super computer is about 3 years old. Of those 38 subjects, 7 exceeded
20 hour time limit on the batch script.  The others took about 12 hours to
finish. All subjects had a 1mm isotropic MPRAGE and FLAIR. Below is the
command I used for one of them. Is there a reason for some subjects
recon-all would take more then 20 hours?


recon-all -s 10016_20170414 -i
/scratch/brierm/Images/10016_20170414_T1.nii -FLAIR
/scratch/brierm/Images/10016_20170414_FLAIR.nii  -FLAIRpial -all
-mprage -hippocampal-subfields-T1 -qcache
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[Freesurfer] Lesion mask

[Aaron Tanenbaum]

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I am working on a project where we are attempting to automate localization
of white matter hyper intensities. So far it looks good. I was wondering is
there a way to feeding this mask to FreeSurfer 6.0  to help improve of the
parcellation and segmentation.
Thank you
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[Freesurfer] T2/Flair benefits in freesurfer 6.0

[Aaron Tanenbaum]

External Email - Use Caution

I am not too sure if I have asked you this question before. I know the use
of a flair or T2 helps with dealing with the dura. I was wondering if there
are other benefits?
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[Freesurfer] Freesurfer 5.3 flags

[Aaron Tanenbaum]

External Email - Use Caution

Hello freesurfers,
Our lab has been using freesurfer 5.3 for a while. We use the following
flag when we run the initial recon-all

-mprage -hippo-subfields -qcache -cortparc3 -parcstats3 -cubic -pctsurfcon
-custom-tal-atlas TRIO_PIB_NDC_as_mni_average_305


However i have found out that we do not use any of these flags when we have
we rerun recon-all after making standard edits. So my question is do any of
these flags need to be used when rerun recon-all?
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Re: [Freesurfer] acquisition protocols 3T Prisma

[Aaron Tanenbaum]

External Email - Use Caution

I would not limit yourself to one person.  I have designed protocols for
multiple studies.  The answer will surprisingly vary depending on your
question.  I would not recommend simply using a protocol that some one
gives you. I have seen very promising studies fail because the PI did not
do enough research over it. On a side note, when you finally have your
protocol, test the whole protocol before you use it for your study. I have
dealt with many projects where a tech did not set the protocol up
correctly, took to long to run, or results was not what they expected.
Though what I have said my sound obvious to you, I say it because I see PIs
not doing it and things go really bad.

On Fri, Oct 19, 2018 at 3:28 PM Glasser, Matthew  wrote:

> External Email - Use Caution
>
> I would particularly recommend the third name on that list, as Mike has
> done a lot of work on the HCP-Style acquisition protocols.
>
> Matt.
>
> From:  on behalf of Aaron
> Tanenbaum 
> Reply-To: Freesurfer support list 
> Date: Friday, October 19, 2018 at 3:23 PM
> To: Freesurfer 
> Subject: Re: [Freesurfer] acquisition protocols 3T Prisma
>
> External Email - Use Caution
>
> I suggest you talk to the folks at Washington university in St Louis.
> There has been considerable amount of work looking at this.  You should
> contact the following individuals
> Steve Petersen  s...@wustl.edu
> Avi Snyder   azsny...@wustl.edu
> Michael harms mha...@wustl.edu
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] acquisition protocols 3T Prisma

[Aaron Tanenbaum]

External Email - Use Caution

I suggest you talk to the folks at Washington university in St Louis. There
has been considerable amount of work looking at this.  You should contact
the following individuals
Steve Petersen  s...@wustl.edu
Avi Snyder   azsny...@wustl.edu
Michael harms mha...@wustl.edu
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[Freesurfer] updateing freesurfer.

[Aaron Tanenbaum]

External Email - Use Caution

I tried updating freesurfer 6.0 using the command fs_update. I get the
following output.



>  Build is freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
>
>Running this will update some of your freesurfer binaries.
>
>  Shall I proceed? [y/n/Abort]: y
>
> rsync -zbrlv --progress --suffix=.1539713469_bak rsync://
> surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c/*
> /data/jsp/human2/fcMRI/Aaron/FreeSurfer/freesurfer_6_0/
> receiving incremental file list
> rsync: change_dir
> "/dist/freesurfer/patches/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c"
> (in pub) failed: No such file or directory (2)
>
> sent 8 bytes  received 173 bytes  362.00 bytes/sec
> total size is 0  speedup is 0.00
> rsync error: some files/attrs were not transferred (see previous errors)
> (code 23) at main.c(1655) [Receiver=3.1.1]
>
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[Freesurfer] wm.mgz values

[Aaron Tanenbaum]

External Email - Use Caution

Hello Freesurfers.

I was wondering of for the purposes of editing wm.mgz if changing
voxel values to anything but 255 and 1 will be useful in anyway. If so
I was wondering if you can explain to me what the following values
mean and how do I use them.



#define THICKEN_FILL 200
#define NBHD_FILL210
#define VENTRICLE_FILL   220
#define DIAGONAL_FILL230
#define DEGENERATE_FILL  240
#define OFFSET_FILTER_FILL   245
#define AUTO_FILL250
#define PRETESS_FILL 215
#define WM_EDITED_ON_VAL 255
#define WM_EDITED_OFF_VAL  1
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Re: [Freesurfer] missing ribbon.mgz

[Aaron Tanenbaum]

External Email - Use Caution

I just noticed that this problem is a now and resolved. I just have to
replace the mri_segstats.
Thank you for your time.


On Fri, Jul 13, 2018 at 6:08 PM Aaron Tanenbaum 
wrote:

> Yes, I first ran autorecon1 and 2 for the initial processing. I then made
> only made brainmask edits followed by running it with autorecon2. The thing
> is that according to this URL
>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
>>
>
> The ribbon.mgz is created in autorecon3, for this reason the file does not
> exist. So why is it being called autorecon2?
>
> On Fri, Jul 13, 2018 at 5:27 PM Glasser, Matthew 
> wrote:
>
>> External Email - Use Caution
>>
>> Did you run the preceding steps of FreeSurfer?  Does that file exist?
>>
>> Peace,
>>
>> Matt.
>>
>> From:  on behalf of Aaron
>> Tanenbaum 
>> Reply-To: Freesurfer support list 
>> Date: Friday, July 13, 2018 at 5:24 PM
>> To: Freesurfer 
>> Subject: [Freesurfer] missing ribbon.mgz
>>
>> External Email - Use Caution
>>
>> I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04.  I
>> am getting an error, see below
>> I am using the command
>>
>> recon-all -s BOLD-52_v1 -mprage -autorecon2
>> This has happened before. What did I do wrong.
>>
>>
>>
>> #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018
>>>
>>> INFO: mri_segstats will not calculate Supratentorial
>>>   due to missing ribbon.mgz file
>>> /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1
>>>
>>>  mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>>> mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
>>> --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz
>>> --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
>>> --surf-ctx-vol --totalgray --euler --ctab
>>> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject
>>> BOLD-52_v1
>>>
>>>
>>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>>> cwd
>>> cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>>> mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
>>> --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz
>>> --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
>>> --surf-ctx-vol --totalgray --euler --ctab
>>> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject
>>> BOLD-52_v1
>>> sysname  Linux
>>> hostname brahms
>>> machine  x86_64
>>> user tanenbauma
>>> UseRobust  0
>>> atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 )
>>> mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz,
>>> -1): could not open file
>>> Computing euler number
>>> orig.nofix lheno =  -70, rheno = -38
>>> orig.nofix lhholes =   36, rhholes = 20
>>> Loading mri/aseg.mgz
>>> Getting Brain Volume Statistics
>>> Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13
>>> 14:54:07 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>>>
>>> recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT
>>> 2018
>>>
>>> To report a problem, see
>>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>>
>>
>>
>>
>>
>>
>> --
>>
>> The materials in this message are private and may contain Protected
>> Healthcare Information or other information of a sensitive nature. If you
>> are not the intended recipient, be advised that any unauthorized use,
>> disclosure, copying or the taking of any action in reliance on the contents
>> of this information is strictly prohibited. If you have received this email
>> in error, please immediately notify the sender via telephone or return mail.
>> ___
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>>
>>
>> The information in this e-mail is intended only for the person to whom it
>> is
>> addressed. If you believe this e-mail was sent to you in error and the
>> e-mail
>> contains patient information, please contact the Partners Compliance
>> HelpLine at
>> http://www.partners.org/complianceline . If the e-mail was sent to you
>> in error
>> but does not contain patient information, please contact the sender and
>> properly
>> dispose of the e-mail.
>>
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Re: [Freesurfer] missing ribbon.mgz

[Aaron Tanenbaum]

External Email - Use Caution

Yes, I first ran autorecon1 and 2 for the initial processing. I then made
only made brainmask edits followed by running it with autorecon2. The thing
is that according to this URL

> https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllDevTable
>

The ribbon.mgz is created in autorecon3, for this reason the file does not
exist. So why is it being called autorecon2?

On Fri, Jul 13, 2018 at 5:27 PM Glasser, Matthew  wrote:

> External Email - Use Caution
>
> Did you run the preceding steps of FreeSurfer?  Does that file exist?
>
> Peace,
>
> Matt.
>
> From:  on behalf of Aaron
> Tanenbaum 
> Reply-To: Freesurfer support list 
> Date: Friday, July 13, 2018 at 5:24 PM
> To: Freesurfer 
> Subject: [Freesurfer] missing ribbon.mgz
>
> External Email - Use Caution
>
> I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04.  I am
> getting an error, see below
> I am using the command
>
> recon-all -s BOLD-52_v1 -mprage -autorecon2
> This has happened before. What did I do wrong.
>
>
>
> #@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018
>>
>> INFO: mri_segstats will not calculate Supratentorial
>>   due to missing ribbon.mgz file
>> /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1
>>
>>  mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz
>> --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0
>> --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm
>> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
>> --euler --ctab /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt
>> --subject BOLD-52_v1
>>
>>
>> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
>> cwd
>> cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
>> mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
>> --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz
>> --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
>> --surf-ctx-vol --totalgray --euler --ctab
>> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject
>> BOLD-52_v1
>> sysname  Linux
>> hostname brahms
>> machine  x86_64
>> user tanenbauma
>> UseRobust  0
>> atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 )
>> mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz,
>> -1): could not open file
>> Computing euler number
>> orig.nofix lheno =  -70, rheno = -38
>> orig.nofix lhholes =   36, rhholes = 20
>> Loading mri/aseg.mgz
>> Getting Brain Volume Statistics
>> Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07
>> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>>
>> recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018
>>
>> To report a problem, see
>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>
>
>
>
>
>
> --
>
> The materials in this message are private and may contain Protected
> Healthcare Information or other information of a sensitive nature. If you
> are not the intended recipient, be advised that any unauthorized use,
> disclosure, copying or the taking of any action in reliance on the contents
> of this information is strictly prohibited. If you have received this email
> in error, please immediately notify the sender via telephone or return mail.
> ___
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[Freesurfer] missing ribbon.mgz

[Aaron Tanenbaum]

External Email - Use Caution

I am a bit puzzled. I am running freesurfer 5.3 HCP on ubuntu 14.04.  I am
getting an error, see below
I am using the command

recon-all -s BOLD-52_v1 -mprage -autorecon2
This has happened before. What did I do wrong.



#@# ASeg Stats Fri Jul 13 12:55:02 CDT 2018
>
> INFO: mri_segstats will not calculate Supratentorial
>   due to missing ribbon.mgz file
> /data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1
>
>  mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv mri/norm.mgz
> --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg --excludeid 0
> --excl-ctxgmwm --subcortgray --in mri/norm.mgz --in-intensity-name norm
> --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray
> --euler --ctab /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt
> --subject BOLD-52_v1
>
>
> $Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $
> cwd
> cmdline mri_segstats --seg mri/aseg.mgz --sum stats/aseg.stats --pv
> mri/norm.mgz --empty --brainmask mri/brainmask.mgz --brain-vol-from-seg
> --excludeid 0 --excl-ctxgmwm --subcortgray --in mri/norm.mgz
> --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol
> --surf-ctx-vol --totalgray --euler --ctab
> /data/ances/FreeSurfer/freesurfer_5_3_HCP//ASegStatsLUT.txt --subject
> BOLD-52_v1
> sysname  Linux
> hostname brahms
> machine  x86_64
> user tanenbauma
> UseRobust  0
> atlas_icv (eTIV) = 1714974 mm^3(det: 1.135939 )
> mghRead(/data/nil-bluearc/ances/Aaron/FreeSurfers/BOLD-52_v1/mri/ribbon.mgz,
> -1): could not open file
> Computing euler number
> orig.nofix lheno =  -70, rheno = -38
> orig.nofix lhholes =   36, rhholes = 20
> Loading mri/aseg.mgz
> Getting Brain Volume Statistics
> Linux brahms 3.19.0-80-generic #88~14.04.1-Ubuntu SMP Fri Jan 13 14:54:07
> UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
>
> recon-all -s BOLD-52_v1 exited with ERRORS at Fri Jul 13 12:55:11 CDT 2018
>
> To report a problem, see
> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>
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Re: [Freesurfer] crypt_gkey = (null)

[Aaron Tanenbaum]

External Email - Use Caution

I checked my system is not encrypted. I had someone else run the command on
the same machine. It worked for them. So I changed my BASH environment to a
default environment. I still get the same error.

I tried this again but with a different FreeSurfer 5.3. turns out the one I
was using has been altered version of FreeSurfer.  I do not know how it was
altered. It worked. so it has to do with the altered FreeSurfer.
I ran the command mri_convert -version  on both FreeSurfer.

for the unaltered i get the out put

*mri_convert -version stable5*
altered version i get

*mri_convert -version dev build (use --all-info flag for full version info)*

with this output i type in mri_convert --all-info
*mri_convert  ProgramArguments: --all-info  ProgramVersion: $Name:  $
TimeStamp: 2018/06/12-18:32:17-GMT  BuildTimeStamp: Aug 22 2014 21:04:47
CVS: $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $  User:
tanenbauma  Machine: rocky  Platform: Linux  PlatformVersion:
3.10.0-862.el7.x86_64  CompilerName: GCC  CompilerVersion: 40400*
Wondering is this version of mri_convert a developmental version?
Also both version are the CentOS 6 build.


On Tue, Jun 12, 2018 at 1:01 PM Dicamillo, Robert <
rdicami...@mgh.harvard.edu> wrote:

> Hello Aaron,
>
> You could check to see if the CentOS 7 system is using disk encryption,
> e.g., if the
> following command return 1, then it would mean encryption is in use (which
> can be
> an issue with FreeSurfer).
>
> $ cat /proc/sys/crypto/fips_enabled
>
> If it returns zero, it could be an issue with a system library like glibc
> on CentOS 7.5
> (that does not happen on older versions of  CentOS).
>
> Either way, this is not your doing ;-)
>
>
> On Jun 12, 2018, at 11:51 AM, Aaron Tanenbaum 
> wrote:
>
> External Email - Use Caution
>
> I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3.
> When i get to the part where MRI_convert is creating the the orig001.mgz
> its gives me a segmentation fault. if i run this on a centos 6 system it
> works fine. below is the output of the program.
>
>
> /data/gizmo/data1/freesurfer5.3/bin/mri_convert
> /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
> /data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
> $Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
> reading from
> /data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
> crypt_gkey = (null)
> Segmentation fault (core dumped)
>
>
>
> Did I do anything wrong?
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[Freesurfer] crypt_gkey = (null)

[Aaron Tanenbaum]

External Email - Use Caution

I am currently running CentOS 7.5 and attempting to run FreeSurfer 5.3.
When i get to the part where MRI_convert is creating the the orig001.mgz
its gives me a segmentation fault. if i run this on a centos 6 system it
works fine. below is the output of the program.


/data/gizmo/data1/freesurfer5.3/bin/mri_convert
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm
/data/anlab/Aaron/JoEtzl_testing/FreeSurfer/Test1/mri/orig/001.mgz
$Id: mri_convert.c,v 1.213 2014/07/29 19:22:31 fischl Exp $
reading from
/data/anlab/Aaron/JoEtzl_testing/Test1/DICOMS/study7/MOCC_AG_002.MR.CCIR-00900_CCIR-0987_Braver.7.27.20180405.144706.1fg9cq4.dcm...
crypt_gkey = (null)
Segmentation fault (core dumped)



Did I do anything wrong?
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[Freesurfer] mri_ca_register

[Aaron Tanenbaum]

External Email - Use Caution

Hello FreeSurfers,
I am trying to find what the -l flag does for the program mri_ca_register
program. Does not seem to be documented anywhere but i could be mistaken.
Aaron Tanenbaum
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[Freesurfer] Using mprage flag.

[Aaron Tanenbaum]

External Email - Use Caution

Hello FreeSurfers
When should I use the MPRAGE flag for recon-all?

Aaron Tanenbaum
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Re: [Freesurfer] Longitudinal Pipeline (fwd)

[Aaron Tanenbaum]

Oh wow. thank you very much. You just save me weeks worth of work.

On Tue, Jan 16, 2018 at 2:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> FYI
>
> -- Forwarded message --
> Date: Tue, 16 Jan 2018 19:59:38 +
> From: Mark Jenkinson <mark.jenkin...@ndcn.ox.ac.uk>
> To: Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> Subject: Re: [Freesurfer] Longitudinal Pipeline
>
> Hi Aaron and Hi Bruce!
> There is code to convert ANTs format to FSL, so you can use that.
> It is part of this tool:
>   https://sourceforge.net/p/c3d/git/ci/master/tree/doc/c3d.md
>
> I've included a code snippet below to show how we've used this.
> Cheers,
> MJ
>
> ${antsFolder}/antsRegistrationSyN.sh -d 3 -f ${ref} -f ${ref2} -m ${src}
> -m ${src2} -o
> ${workdir}/${outname}_ -t 'b' -j 1
>
> ${c3dFolder}/c3d_affine_tool -ref ${ref} -src ${src} -itk
> ${workdir}/${outname}_0GenericAffine.mat
> -ras2fsl -o ${workdir}/${outname}_affine_fsl.mat
>
> ${c3dFolder}/c3d -mcs ${workdir}/${outname}_1Warp.nii.gz -oo
> ${workdir}/wx.nii.gz
> ${workdir}/wy.nii.gz ${workdir}/wz.nii.gz
> ${FSLDIR}/bin/fslmaths ${workdir}/wy -mul -1 ${workdir}/i_wy
> ${FSLDIR}/bin/fslmerge -t ${workdir}/${outname}_warp_fsl ${workdir}/wx
> ${workdir}/i_wy ${workdir}/wz
>
> ${FSLDIR}/bin/convertwarp --ref=${ref} --premat=${workdir}/${outname}
> _affine_fsl.mat
> --warp1=${workdir}/${outname}_warp_fsl --out=${workdir}/${outname}_wa
> rp_fsl
> ${FSLDIR}/bin/invwarp -w ${workdir}/${outname}_warp_fsl -o
> ${workdir}/${refBN}_to_${srcBN}_warp_fsl
> -r ${src}
>
>
>
>   On 15 Jan 2018, at 15:18, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
> wrote:
>
> Hi Aaron
>
> we compute the warp and save it in the mri/transforms/talairach.m3z, but
> don't apply it (so
> don't require an extra resampling). I know we have some tools around to
> convert to ANTS
> format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!)
>
> cheers
> Bruce
>
>
> On Mon, 15 Jan 2018, Aaron Tanenbaum wrote:
>
>   Is the warp saved anywhere and where can I find it? Also is the warp
> compatible
>   with FNIRT in any
>   way. I am interested in combining warps together to reduce the
> number of
>   re-sampling steps.
>   Thank you so much in advanced
>   On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl <
> fis...@nmr.mgh.harvard.edu> wrote:
>in the last stage there is a nonlinear atlas alignment that is
> specific to
>each timepoint. We are working on building a nonlinear base,
> but it is not
>distributed yet.
>
>cheers
>Bruce
>  On Sun, 14 Jan 2018, Aaron
>Tanenbaum wrote:
>
>>
>> I am interested in knowing what type of alignment goes into
> the last stage
>   of the
>longitudinal
>> pipeline. Are each longitudinal time point non-linearly
> aligned to the base
>   image? If
>so can I find
>> the warp?
>>
>>
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Re: [Freesurfer] Longitudinal Pipeline

[Aaron Tanenbaum]

Thank you very much. Your last email gave me a lot to work with.

On Mon, Jan 15, 2018 at 9:18 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> Hi Aaron
>
> we compute the warp and save it in the mri/transforms/talairach.m3z, but
> don't apply it (so don't require an extra resampling). I know we have some
> tools around to convert to ANTS format, but I'm not sure about fnirt. I'll
> cc MJ who may know (hi MJ!)
>
> cheers
> Bruce
>
>
>
> On Mon, 15 Jan 2018, Aaron Tanenbaum wrote:
>
> Is the warp saved anywhere and where can I find it? Also is the warp
>> compatible with FNIRT in any
>> way. I am interested in combining warps together to reduce the number of
>> re-sampling steps.
>> Thank you so much in advanced
>>
>> On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
>> wrote:
>>   in the last stage there is a nonlinear atlas alignment that is
>> specific to
>>   each timepoint. We are working on building a nonlinear base, but it
>> is not
>>   distributed yet.
>>
>>   cheers
>>   Bruce
>> On Sun, 14 Jan 2018, Aaron
>>   Tanenbaum wrote:
>>
>>   >
>>   > I am interested in knowing what type of alignment goes into the
>> last stage of the
>>   longitudinal
>>   > pipeline. Are each longitudinal time point non-linearly aligned
>> to the base image? If
>>   so can I find
>>   > the warp?
>>   >
>>   >
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>>
>>
>>
>>
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Re: [Freesurfer] Longitudinal Pipeline

[Aaron Tanenbaum]

Is the warp saved anywhere and where can I find it? Also is the warp
compatible with FNIRT in any way. I am interested in combining warps
together to reduce the number of re-sampling steps.
Thank you so much in advanced

On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu>
wrote:

> in the last stage there is a nonlinear atlas alignment that is specific to
> each timepoint. We are working on building a nonlinear base, but it is not
> distributed yet.
>
> cheers
> Bruce
>   On Sun, 14 Jan 2018, Aaron
> Tanenbaum wrote:
>
> >
> > I am interested in knowing what type of alignment goes into the last
> stage of the longitudinal
> > pipeline. Are each longitudinal time point non-linearly aligned to the
> base image? If so can I find
> > the warp?
> >
> >
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[Freesurfer] Longitudinal Pipeline

[Aaron Tanenbaum]

I am interested in knowing what type of alignment goes into the last stage
of the longitudinal pipeline. Are each longitudinal time point non-linearly
aligned to the base image? If so can I find the warp?
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[Freesurfer] Description of a few files generated by

[Aaron Tanenbaum]

I would like to get a clarification on what some the the files generated by
FreeSurfer recon-all

based on the URL
https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles

The web pages says the nu.mgz  "This is a intensity normalized volume
generated after correcting for non-uniformity in the orig.mgz".  I just
need a clarification the intensity normalized is just a global scaling and
the correction for non-uniformity is the bias field correction. I was
wondering if the orig.mgz is bias field corrected to generate the
orig_nu.mgz and the intensity normalized to generate the nu.mgz.

Finally what is the norm.mgz image. I cannot final details on how it is
created.
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[Freesurfer] patching 5.1

[Aaron Tanenbaum]

Hello All
Several years ago Freesurfer 5.1 was patched to resolve some issues.  I
just remember the patch resolved issues plaguing 5.1 and earlier. how does
one get the patch version. no where on the FTP server i can see patched
versions and instruction on performing a patch.
Aaron Tanenbaum
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[Freesurfer] break up time course nifti

[Aaron Tanenbaum]

hola freesurfers,
I have a time course surface nii files. I would like to break up the time
course into many nii files for each time frame. Is there an easy way of
doing this.
Thank you
Aaron Tanenbaum
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[Freesurfer] converting a volume to a surface

[Aaron Tanenbaum]

Hola Freesurfers,
I am new to Freesurfer and still learning the basics. I have been given a
project and have not found a way to do it. Part of this task involves
taking a 4dfp volume time series and convert it to a time series of a
surface. This 4dfp I have is a statistical analysis mapped on to a specific
atlas volume.  Does anyone know of a way to do this. Any help will be
highly appreciated.
Gracias
Aaron Tanenbaum
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.