Re: [Freesurfer] InfantFS - resampling asset to native space

2021-12-08 Thread Fateme Haghpanah 
External Email - Use Caution

Thank you so much!

> On Dec 7, 2021, at 12:06 PM, Zollei, Lilla,Ph.D.  
> wrote:
> 
> Hi Fateme,
> Infant Freesurfer takes a single input image so there is no rawavg file 
> created at the beginning of the pipeline. You should be able to replace 
> rawavg in your command with the original image that you used as an input.
> Lilla
> 
> 
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  on behalf of Fateme Haghpanah 
> 
> Sent: Wednesday, December 1, 2021 9:43 AM
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: [Freesurfer] InfantFS - resampling asset to native space
> 
>External Email - Use Caution
> 
> Dear FreeSurfer Developers,
> 
> We are using InfantFS and noticed that after running recon-all 
> ("infant_recon_all --newborn --s ${SUBJ}”) , the voxel size changes to 1*1*1. 
> I know that using "mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 
> aseg-in-rawavg.mgz --regheader aseg.mgz” we can convert the aseg output of 
> adult FreeSurfer to native space. Is there any similar command to do so for 
> infants?
> 
> I wanted to try this one, however there is no rawavg.mgz file in the mri 
> folder of infant subjects.
> 
> Thanks in advance,
> Fateme
> 
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Re: [Freesurfer] Propagating hippocampal subfield segmentation to native T2w space

2021-12-08 Thread Iglesias Gonzalez, Juan E. 
Dear Michael,

Your code will create 3DT2.FSspace.mgz which is at 0.55mm resolution but with a 
 rotation/translation  in the header to overlap the T1 in RAS space.

You can now run
mri_convert [lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz   
[lr]h.hippoAmygLabels-T1.v21.[hierarchy].resampled.mgz -rl 3DT2.FSspace.mgz -rt 
nearest -odt float
to produce a volume in the same space as 3DT2.FSspace.mgz (also at 0.55mm). The 
flat -rl stands for “replace like”.

At that point, if the rotation between the original T2 and 3DT2.FSspace.mgz 
bothers you, you can combine the voxels from 
[lr]h.hippoAmygLabels-T1.v21.[hierarchy].resampled.mgz and combine them with 
the header of the original T2 to undo the rotation ;-)

Cheers,

/E

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Dec 8, 2021, at 04:33, Eyre, Michael 
mailto:michael.e...@kcl.ac.uk>> wrote:

External Email - Use Caution

Hi all

Regarding hippocampal subfield segmentation in FS7- how can I move the 
segmentation result to native T2w space? I plan to compare the result with a 
manual segmentation which was done in this space, using scripts which require 
nifti inputs.

I have run FS7 specifying with the -cm flag that this takes place in my T1 
(MP2RAGE) 0.65mm isotropic resolution:
recon-all -all -s  -i T1w.nii -T2 T2w.nii -T2pial -gcut -cm

Then I ran the Hc subfield segmentation, specifying that my T2w volume 
(3D-SPACE, 0.55mm isotropic) should be used for this:
segmentHA_T2.sh  T2w.nii 3DT2 0

The output that I want to move back to native 3DT2 space is the labelled volume 
lh.hippoAmygLabels-3DT2.v21.mgz (or the nifti of this which of course I can 
create using mri_convert). However this volume is 0.333mm isotropic and has a 
limited field of view - from the documentation: "Note that 
[lr]h.hippoAmygLabels-T1.v21.mgz and 
[lr]h.hippoAmygLabels-T1.v21.[hierarchy].mgz cover only a patch around the 
hippocampus, at a higher resolution than the input image."

The most relevant guidance I can find in the documentation is 
"[lr]h.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz live in the same voxel space as 
the other Freesurfer volumes (e.g., orig.mgz, nu.mgz, aseg.mgz), so you can use 
it directly to produce masks for further analyses, but its resolution is lower 
(1 mm vs 0.333 mm)." In my case FSvoxelSpace is at 0.65mm resolution, but this 
is still lower than my T2w volume (0.55mm) and so would involve some 
downsampling (0.333mm --> 0.65mm --> 0.55mm) which I would like to avoid.

I have tried various linear registration approaches but I always end up with a 
result which, although in 0.55mm space, is clearly not aligned with the 
hippocampus when viewed together with my T2w.nii in ITK-SNAP.

Any suggestions would be much appreciated!

Many thanks

Mike
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Re: [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals file

2021-12-08 Thread fsbuild 
External Email - Use Caution

Hello Jürgen,
Try running the bash shell from the terminal, e.g., before running anything 
type,
$ bash
- and then try your command again.
If that works then I would set your login shell to bash (as the default is 
dash).

- R.
On Dec 7, 2021, at 01:46, juergen.haen...@upd.unibe.ch 
wrote:External Email - Use 
CautionDear Anastasiathank a 
lot for the answer.We use Ubuntu 18.04..6 LTS.When we run the command directly 
in the terminalbedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmriwe
 get the sane error/usr/local/freesurfer/bin/bedpostx_mgh: 128: 
/usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(„ unexpectedwhen we run 
the command you sent in your last email, i.e. fslver=(`cat 
$FSLDIR/etc/fslversion | sed 's/\./ /g’`)we get the following errorBadly placed 
()’s.Thanks in advanceRegardsJürgenAm 03.12.2021 um 00:02 schrieb Yendiki, 
Anastasia :Hi Jürgen - I haven't 
been able to replicate your error locally. What operating system are you 
running it on? And what do you see if you try run the line that errors out 
directly on the command line? The line is:fslver=(`cat $FSLDIR/etc/fslversion | 
sed 's/\./ 
/g'`)Thanks,Anastasia.From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 
of juergen.haen...@upd.unibe.ch Sent: Thursday,
 November 25, 2021 1:40 
AMTo: freesurfer@nmr.mgh.harvard.edu Subject: Re:
 [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals 
file External Email - Use 
CautionDear Anastasiacat 
$FSLDIR/etc/fslversion reported6.0.5.1:57b01774I guess its the newest version 
availableThanksJürgenAm 24.11.2021 um 15:53 schrieb Yendiki, Anastasia 
:Hi Jürgen - Can you check what's in this file: 
$FSLDIR/etc/fslversion 
?Thanks,Anastasia.From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 
of juergen.haen...@upd.unibe.ch Sent: Wednesday,
 November 24, 2021 12:53 
AMTo: freesurfer@nmr.mgh.harvard.edu Subject: Re:
 [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals 
file External Email - Use 
CautionDear Anastasiawhen I 
type $FSLDIR in the terminal, I get /usr/local/fsl: permission denied.this is 
the right path where fsl is installed.however, I can start FSL GUI and also 
other FSL commands.Best JürgenAm 24.11.2021 um 01:20 schrieb Yendiki, Anastasia 
:Hi Jürgen - What's your $FSLDIR set 
to?Anastasia.From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf 
of juergen.haen...@upd.unibe.ch Sent: Tuesday,
 November 23, 2021 9:36 
AMTo: freesurfer@nmr.mgh.harvard.edu Subject: Re:
 [Freesurfer] TRACULA error wrt to dwi_orig_las.1.bvals 
file External Email - Use 
CautionDear Anastasiathank you 
for the new option. It works. Now we were able to finish trac-all -prep without 
any further problem.However, when we try to run trac-all -bedp, the following 
error occurred:--trac-all -bedp -c 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/tracula_config_IPS_all_example_DICOM_NIFTI_ANTs.txtINFO:
 SUBJECTS_DIR is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_FS_subjectsINFO:
 Diffusion root is 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720Actual
 FREESURFER_HOME /usr/local/freesurferln -sf 
.../dlabel/diff/aparc+aseg_mask.bbr.nii.gz 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/nodif_brain_mask.nii.gzWARN:
 Running bedbostx locally - this might take a whileWARN: It is recommended to 
run this step on a clusterbedpostx_mgh -n 2 -model 1 
/mnt/981dac6a-ec33-4a79-9c9e-588e004c6806/Juergen/01_IPS_Project/DTI_DATA/03_TRACULA_Test/00_TRACULA_Results_DICOMs_NIFTIs_FS720/IPS_CO_007_ANTs/dmri/usr/local/freesurfer/bin/bedpostx_mgh:
 128: /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" 
unexpected——we have found this message from 2014 MailScanner has 
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[Freesurfer] Hippocampal Subfield data not populating

2021-12-08 Thread Taylor, Lisa 
External Email - Use Caution

Hi,

Sorry if this email has been seen. I got an automatic response that my previous 
emails were in the queue waiting to be approved due to the email size, but 
haven't seen an approval yet. So, I am trying again without the email 
attachments (both recon all and hippocampal subfield log files) to see if it 
might be more efficient this way.

Running the hippocampal-subfields-T1 argument for some reason is not populating 
the data I need. My recon-all log says it was exited without error, and my 
hippocampal subfield log file seems to have run smoothly except for this one 
line that I am not sure is telling or not:

/data/opt/apps/freesurfer/6.0.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 46:  2066 Killed  
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args

Please advise!

Thank you.

Lisa



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Re: [Freesurfer] Hippocampal Subfield data not populating

2021-12-08 Thread Iglesias Gonzalez, Juan E. 
Dear Lisa,
It’s difficult to tell without seeing the logs, but it seems like you ran out 
of RAM memory?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://www.jeiglesias.com

On Dec 8, 2021, at 15:57, Taylor, Lisa 
mailto:ltayl...@hs.uci.edu>> wrote:

External Email - Use Caution

Hi,

Sorry if this email has been seen. I got an automatic response that my previous 
emails were in the queue waiting to be approved due to the email size, but 
haven't seen an approval yet. So, I am trying again without the email 
attachments (both recon all and hippocampal subfield log files) to see if it 
might be more efficient this way.

Running the hippocampal-subfields-T1 argument for some reason is not populating 
the data I need. My recon-all log says it was exited without error, and my 
hippocampal subfield log file seems to have run smoothly except for this one 
line that I am not sure is telling or not:

/data/opt/apps/freesurfer/6.0.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 46:  2066 Killed  
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args

Please advise!

Thank you.

Lisa



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hacomplia...@uci.edu or by phone 888-456-7006 
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cannot be guaranteed to be secure or error-free as information could be 
intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain 
viruses. The sender therefore does not accept liability for any errors or 
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Re: [Freesurfer] Hippocampal Subfield data not populating

2021-12-08 Thread Taylor, Lisa 
External Email - Use Caution

Hi Juan,

My email response to you has the attachments of the log files, but it once 
again is being held for moderator approval. Not sure how often or who checks 
it, but my last few emails are there waiting 🙂

Thank you again for your help. Hopefully, the email can be approved with the 
log files so they can be reviewed.

Lisa

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Iglesias Gonzalez, Juan 
E. 
Sent: Wednesday, December 8, 2021 1:00 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Hippocampal Subfield data not populating

Dear Lisa,
It’s difficult to tell without seeing the logs, but it seems like you ran out 
of RAM memory?
Cheers,
/Eugenio

Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
http://secure-web.cisco.com/1sNxoZ5Oy64QvlP-IJ_xchsLgpk3s4tD-j00cjSUwEW380zHaYb1mtIxdgSCh6_SSp6mSkkA_mn_pG_lFxiMaSl3KnFV6ZqDh4BAH2-qgyzf6dwN8fvkWYbggXAbVSCQUf8E6d_uc5j6mkdeWs__RKlCJSqEA0s2JYp2v6eA8gRAzPZ1bPTZwyZ3-DohQjrVuKwgVglT57UhcZIMpZpp6HPjTDYJeSvDpSvndwvKOFxZyGgf61pgK6wzYpjyHLxG08iN2h8T9m8HU3Q93XrpsmATsoQLt0qdhEDJjTAov3Y7gEssCcqNM1DcHN6W6zV14/http%3A%2F%2Fwww.jeiglesias.com

On Dec 8, 2021, at 15:57, Taylor, Lisa 
mailto:ltayl...@hs.uci.edu>> wrote:

External Email - Use Caution

Hi,

Sorry if this email has been seen. I got an automatic response that my previous 
emails were in the queue waiting to be approved due to the email size, but 
haven't seen an approval yet. So, I am trying again without the email 
attachments (both recon all and hippocampal subfield log files) to see if it 
might be more efficient this way.

Running the hippocampal-subfields-T1 argument for some reason is not populating 
the data I need. My recon-all log says it was exited without error, and my 
hippocampal subfield log file seems to have run smoothly except for this one 
line that I am not sure is telling or not:

/data/opt/apps/freesurfer/6.0.1/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
 line 46:  2066 Killed  
"${exe_dir}"/segmentSubjectT1_autoEstimateAlveusML $args

Please advise!

Thank you.

Lisa



This message may contain confidential information and is for the sole use of 
the intended recipient(s). If you are not the intended recipient, do not use, 
distribute, or copy this e-mail. Please notify the UC Irvine Health – 
Compliance and Privacy Office via email at 
hacomplia...@uci.edu or by phone 888-456-7006 
immediately if you have received this e-mail in error. E-mail transmission 
cannot be guaranteed to be secure or error-free as information could be 
intercepted, corrupted, lost, destroyed, arrive late or incomplete, or contain 
viruses. The sender therefore does not accept liability for any errors or 
omissions in the contents of this message, which arise as a result of e-mail 
transmission.
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Re: [Freesurfer] Tracula error

2021-12-08 Thread Yendiki, Anastasia 
Hi Mona - Here's how you add something to your Unix path:
https://unix.stackexchange.com/questions/3809/how-can-i-make-a-program-executable-from-everywhere

In your case you'd replace /path/to/file with $ANTSPATH.

Anastasia.



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Nasiriavanaki, Zahra,M.D. 

Sent: Tuesday, December 7, 2021 1:30 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Tracula error

Hi Anastasia,

I did add the ANTs to my path, but am still getting that same error.

I adde the path : setenv ANTSPATH /usr/pubsw/packages/ANTS/2.3.4/bin to the 
.csh file which has all the TRACULA configuration info, and also to the bash 
script that I’m running the trac-all from: export 
ANTSPATH=/usr/pubsw/packages/ANTS/2.3.4/bin

Is there anything else I should do?

Thanks,
Mona


On Dec 6, 2021, at 10:44 AM, Yendiki, Anastasia 
mailto:ayend...@mgh.harvard.edu>> wrote:

Hi Mona - You need to add the location of the ANTs executables to your path.

Best,
Anastasia.


From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Nasiriavanaki, Zahra,M.D. 
mailto:znasiriavan...@mgh.harvard.edu>>
Sent: Sunday, December 5, 2021 12:21 PM
To: freesurfer@nmr.mgh.harvard.edu 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Tracula error

Hello,

I’ve been running the trac-all -prep step and I faced this error:

ConvertTransformFile 3 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.mat
 
/autofs/cluster/guptagp/zn025/ALD/subjects/1/dmri/xfms/diff2syn0GenericAffine.txt
 --hm --ras
ConvertTransformFile: Command not found.
Linux bee.nmr.mgh.harvard.edu 
3.10.0-1160.31.1.el7.x86_64 #1 SMP Thu Jun 10 13:32:12 UTC 2021 x86_64 x86_64 
x86_64 GNU/Linux

trac-preproc exited with ERRORS at Fri Dec  3 14:29:56 EST 2021

Could you please let me know what the problem is? I’m running it in dev 
environment.

Thanks,
Mona


Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry | MGH/HMS
Department of Radiology | MGH/HMS
149 13th Street, 149-2615
Boston, MA, USA, 02129

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[Freesurfer] auto-configure TRACULA for BIDS data

2021-12-08 Thread Yendiki, Anastasia 
Dear FreeSurfers - There's a new script in the development version called 
dmri_bids_config. You can get it here:
https://raw.githubusercontent.com/freesurfer/freesurfer/dev/scripts/dmri_bids_config

There is documentation here:
https://surfer.nmr.mgh.harvard.edu/fswiki/dmri_bids_config

It will parse the BIDS directory structure, find all the DWI scans (and field 
maps, if any), and generate the TRACULA configuration file for you. With this 
file, you can then run TRACULA to pre-process the DWIs and reconstruct tracts 
of interest.

As an added bonus, it will also generate an FSGD file, based on the 
participants.tsv file in your input BIDS directory. The FSGD file can be used 
for stats with mri_glmfit.

It'd be great to have people test this script on their BIDS datasets and report 
any issues. Both legacy and newer data welcome!

Thanks,
Anastasia.



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addressed. If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at http://www.massgeneralbrigham.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.
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.