date:20200720

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

2020-07-20 Thread Alina Rojas

External Email - Use Caution

Thank you, the ciftify was run successfully! But now I have questions to the 
wb-command -cifti-parcellate:
wb_command -cifti-parcellate
   - the cifti file to parcellate
   - a cifti label file to use for the parcellation
   - which mapping to parcellate (integer, ROW, or COLUMN)
   - output - output cifti file
I understand that   should be 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
 but what should I use as label? The 
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii 
from https://balsa.wustl.edu/WN56?  And the 
output from the -cifty-parcellate is .pscalar.nii..how do I get from there to 
GIFTI?

And for the GIFTY to .annot I would do:

  mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer 
example)

Thank you,

Alina

> Am 14.07.2020 um 16:17 schrieb Glasser, Matthew :
> 
>External Email - Use Caution
> 
> I would find using something like ciftify 
> (https://github.com/edickie/ciftify) potentially more straightforward (and 
> then you can just use wb_command -cifti-parcellate on 
> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
>   It is possible to go the other direction too (e.g. using this link: 
> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
>  and then perhaps someone on the list can explain how to go from GIFTI on 
> fsaverage to .annot on the native meshes and extract the stats.
> 
> Matt.
> 
> On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of 
> Alina Rojas"  alinacol...@gmail.com> wrote:
> 
>* External Email - Caution *
> 
>External Email - Use Caution
> 
>Hello Freesurfer support list,
> 
>I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
> subjects to get the values of the parcellation, like aparc.stats but aparc 
> being HCP-MMP1. The aim ist to compare the cortical thickness of the 
> Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
> archive and didn’t find the solution. It would be so great if you could help 
> me!
> 
>Thank you and regards,
> 
>Alina Rojas
> 
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> 
> 
> 
> 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] HCP-MMP1 Parcellation to individual brain for stats

2020-07-20 Thread Glasser, Matthew

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I would use https://balsa.wustl.edu/file/show/3VLx which is the CIFTI label 
file.  The pscalar is not a label file, but rather the average thicknesses in 
each cortical area.  You can view the average thicknesses in Connectome 
Workbench or print out the results with wb_command -cifti-convert -to-text.

Matt.

From:  on behalf of Alina Rojas 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 4:32 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution
Thank you, the ciftify was run successfully! But now I have questions to the 
wb-command -cifti-parcellate:

wb_command -cifti-parcellate

   - the cifti file to parcellate

   - a cifti label file to use for the parcellation

   - which mapping to parcellate (integer, ROW, or COLUMN)

   - output - output cifti file
I understand that   should be 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
 but what should I use as label? The 
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii 
from https://balsa.wustl.edu/WN56? And the output from the -cifty-parcellate is 
.pscalar.nii..how do I get from there to GIFTI?

And for the GIFTY to .annot I would do:

  mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer 
example)

Thank you,

Alina

Am 14.07.2020 um 16:17 schrieb Glasser, Matthew 
mailto:glass...@wustl.edu>>:

   External Email - Use Caution

I would find using something like ciftify (https://github.com/edickie/ciftify) 
potentially more straightforward (and then you can just use wb_command 
-cifti-parcellate on 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
  It is possible to go the other direction too (e.g. using this link: 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
 and then perhaps someone on the list can explain how to go from GIFTI on 
fsaverage to .annot on the native meshes and extract the stats.

Matt.

On 7/14/20, 8:54 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Alina Rojas" 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of alinacol...@gmail.com> wrote:

   * External Email - Caution *

   External Email - Use Caution

   Hello Freesurfer support list,

   I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
subjects to get the values of the parcellation, like aparc.stats but aparc 
being HCP-MMP1. The aim ist to compare the cortical thickness of the 
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
archive and didn’t find the solution. It would be so great if you could help me!

   Thank you and regards,

   Alina Rojas

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or the taking of any action in reliance on the contents of this information is 
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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

2020-07-20 Thread Alina Rojas

External Email - Use Caution

Thank you for the quick answer! For the archive and my understanding…the 
pscalar gives out a column with 360 values, these values are the average 
thickness of my one subject and finally, the data I was searching for: cortical 
thickness values from my subject obtained with Freesurfer but with the 
parcellation of the HCP-MMP1. Is there a document or a command where I can 
correlate these values with the name/number of cortical area?

Regards,

Alina

> Am 20.07.2020 um 11:32 schrieb Alina Rojas :
> 
> Thank you, the ciftify was run successfully! But now I have questions to the 
> wb-command -cifti-parcellate:
> wb_command -cifti-parcellate
>- the cifti file to parcellate
>- a cifti label file to use for the parcellation
>- which mapping to parcellate (integer, ROW, or COLUMN)
>- output - output cifti file
> I understand that   should be 
> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
>  but what should I use as label? The 
> Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii 
> from https://balsa.wustl.edu/WN56?  And the 
> output from the -cifty-parcellate is .pscalar.nii..how do I get from there to 
> GIFTI?
> 
> And for the GIFTY to .annot I would do:
> 
>   mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer 
> example)
> 
> Thank you,
> 
> Alina
> 
>> Am 14.07.2020 um 16:17 schrieb Glasser, Matthew > >:
>> 
>>External Email - Use Caution
>> 
>> I would find using something like ciftify 
>> (https://github.com/edickie/ciftify ) 
>> potentially more straightforward (and then you can just use wb_command 
>> -cifti-parcellate on 
>> ${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
>>   It is possible to go the other direction too (e.g. using this link: 
>> https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
>>  
>> 
>>  and then perhaps someone on the list can explain how to go from GIFTI on 
>> fsaverage to .annot on the native meshes and extract the stats.
>> 
>> Matt.
>> 
>> On 7/14/20, 8:54 AM, "freesurfer-boun...@nmr.mgh.harvard.edu 
>>  on behalf of Alina Rojas" 
>> >  on behalf of 
>> alinacol...@gmail.com > wrote:
>> 
>>* External Email - Caution *
>> 
>>External Email - Use Caution
>> 
>>Hello Freesurfer support list,
>> 
>>I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
>> subjects to get the values of the parcellation, like aparc.stats but aparc 
>> being HCP-MMP1. The aim ist to compare the cortical thickness of the 
>> Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
>> archive and didn’t find the solution. It would be so great if you could help 
>> me!
>> 
>>Thank you and regards,
>> 
>>Alina Rojas
>> 
>>___
>>Freesurfer mailing list
>>Freesurfer@nmr.mgh.harvard.edu 
>>https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> 
>> 
>> 
>> 
>> 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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> 

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[Freesurfer] Error for version 7.1.0 when run the recon-all

2020-07-20 Thread Yang Molly

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Hi list,

I tried to run the latest version Freesurfer (7.1.0) on the Ubantu 18.04
system. I downloaded the “freesurfer-linux-centos7_x86_64-7.1.0.tar.gz” and
successfully installed. I tried to run "recon-all -s bert -autorecon1" and
the terminal replied as "recon-all -s bert finished without error ".
However, when I tried to run the recon-all use the common" recon-all -i
/home/molly/FStry/preA063/preA063.nii -s sub063 -all", the terminal replied

"Traceback (most recent call last):

  File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in


file.write(arg + '\n')

UnicodeEncodeError: 'ascii' codec can't encode character '\udc87' in
position 12: ordinal not in range(128)

ERROR: could not configure recon-all parameters"

I did not retrieve a similar question in the previous mailing list and hope
to get your help.

Thank you

Molly
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[Freesurfer] Flag(s) for parallel processing

2020-07-20 Thread Billah, Tashrif

Hi Douglas,


You asked a good question which prompted me to do an experiment with just 
"-threads 8 -itkthreads 8".

The run time has been quite slower (~8 hours) compared to ~5 hours it took with 
"-parallel -openmp 8".

I agree with you about the underestimation of run time with the latter flags in 
that page. Though the page stipulates

3 hours, I have never been able to get a freesurfer done in less than 5 hours. 
Maybe it is related to the resolution of my

data?


-Tashrif

.


-parallel -openmp 4


should run things with 4 processors and parallelize across hemi where it can 
The run time on that page is probably not accurate. But is it faster when you 
use those options?

On 7/16/2020 11:47 PM, Billah, Tashrif wrote:


This says "-openmp 
 after -parallel", this 
 says "export 
ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=2", while this 
 says "--threads nthreads" 
for parallel processing. I want to run recon-all and want all processes under 
recon-all to be parallelized. Which one(s) of the above flags should I provide 
with recon-all? Please note that the values are not my interest, the flags are. 
I know the proper values I should choose for the flags on my machines.

So far I have been trying "-parallel -openmp 4" option only but my run time 
stays over 5 hours contrary to less than 3 hours stipulated in the 
documentation.

-Tashrif
.

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[Freesurfer] PetSurfer Crashing

2020-07-20 Thread Crawford, Anna

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Hello,


I am trying to run the PetSurfer process for the first time. I was able to run 
gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, 
it is crashing, but I am not sure why. The command I am using and output are 
below. Do you have any guidance as to what is going wrong?


Thank you,

Anna



mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 
6 --seg subject/mri/gtmseg.mgz  --default-seg-merge --auto-mask PSF .01 --mgx 
.01 --o subject/gtmpvc.output
Loading input ../CTPET/PET.template.nii.gz
  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/
cd /mnt/autofs/netRAID18/7T/study709/S2sdt
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 
6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 
.01 --o subject/gtmpvc.output
sysname  Linux
hostname fmri15
machine  x86_64
user crawforda
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
20 avail.processors, using 1
Creating output directory subject/gtmpvc.output
Loading seg for gtm subject/mri/gtmseg.mgz
Loading seg ctab subject/mri/gtmseg.ctab
Reading subject/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
done with seg vol
maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Automask, reducing FOV
region 256 256 109 reduced to 21 11 3  235 245 106
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.97615814209e-01 0.000e+00 -8.381903171539307e-09 
-7.62939453125e-06
7.450580596923828e-09 9.98807907104e-01 0.000e+00 
0.000e+00
-7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 
-1.52587890625e-05
0.000e+00 0.000e+00 0.000e+00 
9.99403953552e-01
src volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 -2.000e+01
dst volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 -2.000e+01
subject subject
fscale 0.15
LTA 1 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.99403953552e-01 0.000e+00 0.000e+00 
-2.09237060547e+01
0.000e+00 9.99403953552e-01 0.000e+00 
-1.10762939453e+01
0.000e+00 0.000e+00 1.000e+00 
-3.000e+00
0.000e+00 0.000e+00 0.000e+00 
1.000e+00
src volume info
valid = 1  # volume info valid
filename = ../CTPET/PET.template.nii.gz
volume = 256 256 109
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 0.000e+00
yras   = -0.000e+00 1.000e+00 0.000e+00
zras   = -0.000e+00 -0.000e+00 1.000e+00
cras   = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03
dst volume info
valid = 1  # volume info valid
filename =
volume = 235 245 106
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 0.000e+00
yras   = -0.000e+00 1.000e+00 0.000e+00
zras   = -0.000e+00 -0.000e+00 1.000e+00
cras   = -1.861288452148438e+01 1.840597229003906e+02 1.250690063476562e+03
--
Data load time 10.9 sec
nmask = 3714389, nsegs = 100, excluding segid=0
FWHM: 6 6 6
Std:  2.54797 2.54797 2.54797
nPad 10, PadThresh 0.0001
Checking Ref Ids
Segmentations used for rescaling
 174 Pons
Computing Seg PVF
Segmentation fault (core dumped)


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Re: [Freesurfer] Right and left on MRI scan and on images

2020-07-20 Thread Douglas Greve

This information is extracted out of the dicom header, so as long as you 
are converting directly from dicom, the information will be correct. You 
can run

mri_info orig.mgz
and it will print out a lot of information, including the orientation 
string. Eg, RAS means that the fastest (column) dimension increases to 
the right. When you look at a volume in freeview, you will see 
coordinates in the control window. These will be RAS


On 7/17/20 7:45 PM, Cibele Bandeira wrote:


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Hello,
I have an MRI sample collected on a Siemens Magnetom Spectra 3T 
scanner. However, we do not place any pointing devices inside the 
scanner to indicate which side is the right and which is the left. I 
was wondering how the images were acquired -  from the front of the 
individuals, meaning that the left in the image is the right in the 
patient? Or otherwise?
When processing the T1-weighted images on Freesurfer, I also have a 
doubt...  the DICOM images are synchronized? Left in DICOM is left in 
the patient? And after freesurfer preprocessing? It flips the images 
or not?


Thank you very much!
--
*Cibele Edom Bandeira*
Doutoranda em Genética e Biologia Molecular (PPGBM)
Universidade Federal do Rio Grande do Sul (UFRGS)


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Re: [Freesurfer] Fwd: One hemisphere recon-all ERROR

2020-07-20 Thread Douglas Greve

sorry, I thought I answered this a while back. Try using -hemi lh 
instead of -lh


On 7/18/20 1:22 PM, Alina Rojas wrote:


External Email - Use Caution

Hello Freesurfer community,

I was wondering if you could look at the e-mail below. Thank you!

Alina


Anfang der weitergeleiteten Nachricht:

*Von: *Alina Rojas mailto:alinacol...@gmail.com>>
*Betreff: **One hemisphere recon-all ERROR*
*Datum: *13. Juli 2020 um 15:25:18 MESZ
*An: *Freesurfer support list >


Hello Freesurfer community,

I'm attempting to compare the cortical thickness of one side of the 
brain between stroke subjects. I got "ERROR: you must include rh 
white and pial surfaces“. I used recon-all -sd 
${TARGET_FOLDER}-subjid $SUBJECTID-i $T1-T2 $T2-qcache-all -3T 
-T2pial -lh. I attached the recon-all.log file. Ist it a way to get 
the aparc?


Thank you for your help,

Alina Rojas





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Re: [Freesurfer] PetSurfer Crashing

2020-07-20 Thread Douglas Greve

Did you really mean to pass subject/mri/gtmseg.lta ? The registration is 
supposed to be the registration of the input (PET.template.nii.gz) to 
the anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz 
to the anatomical.


On 7/20/20 11:21 AM, Crawford, Anna wrote:


External Email - Use Caution

Hello,


I am trying to run the PetSurfer process for the first time. I was 
able to run gtmseg and mri_coreg which seemed to go okay. When I tried 
running mri_gtmpvc, it is crashing, but I am not sure why. The command 
I am using and output are below. Do you have any guidance as to what 
is going wrong?



Thank you,

Anna



mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg 
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz  
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o 
subject/gtmpvc.output

Loading input ../CTPET/PET.template.nii.gz
  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/
cd /mnt/autofs/netRAID18/7T/study709/S2sdt
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg 
subject/mri/gtmseg.lta --psf 6 --seg subject/mri/gtmseg.mgz 
--default-seg-merge --auto-mask PSF .01 --mgx .01 --o 
subject/gtmpvc.output

sysname  Linux
hostname fmri15
machine  x86_64
user crawforda
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
20 avail.processors, using 1
Creating output directory subject/gtmpvc.output
Loading seg for gtm subject/mri/gtmseg.mgz
Loading seg ctab subject/mri/gtmseg.ctab
Reading subject/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
done with seg vol
maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Automask, reducing FOV
region 256 256 109 reduced to 21 11 3  235 245 106
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.97615814209e-01 0.000e+00 -8.381903171539307e-09 
-7.62939453125e-06
7.450580596923828e-09 9.98807907104e-01 0.000e+00 
0.000e+00
-7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 
-1.52587890625e-05
0.000e+00 0.000e+00 0.000e+00 
9.99403953552e-01

src volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 
-2.000e+01

dst volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 
1.000e+00
xras   = -1.000e+00 0.000e+00 
0.000e+00
yras   = 0.000e+00 0.000e+00 
-1.000e+00

zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 
-2.000e+01

subject subject
fscale 0.15
LTA 1 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.99403953552e-01 0.000e+00 0.000e+00 
-2.09237060547e+01
0.000e+00 9.99403953552e-01 0.000e+00 
-1.10762939453e+01
0.000e+00 0.000e+00 1.000e+00 
-3.000e+00
0.000e+00 0.000e+00 0.000e+00 
1.000e+00

src volume info
valid = 1  # volume info valid
filename = ../CTPET/PET.template.nii.gz
volume = 256 256 109
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 
2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 
0.000e+00
yras   = -0.000e+00 1.000e+00 
0.000e+00
zras   = -0.000e+00 -0.000e+00 
1.000e+00

cras   = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03
dst volume info
valid = 1  # volume info valid
filename =
volume = 235 245 106
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 
2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 
0.000e+00
yras   = -0.000e+00 1.000e+00 
0.000e+00
zras   = -0.000e+00 -0.000e+00 
1.000e+00
cras   = -1.861288452148438e+01 1.840597229003906e+02 
1.250690063476562e+03

--
Data load time 10.9 sec
nmask = 3714389, nsegs = 100, excluding segi

[Freesurfer] T2 or FLAIR data to improve pial surfaces

2020-07-20 Thread Batra, Vinita R.

External Email - Use Caution

Dear FreeSurfer experts,

I have both T2 and FLAIR images for the majority of the subjects in my study,
and I want to use them to improve pial surface reconstruction during recon-all
as explained in [1].

My questions are:

1) In general, should I prefer FLAIR over T2, or the other way around?
2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a
T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for 
others, in the same study? We will perform manual QC after the recon-all run 
and exclude bad quality images so I wanted to hear your opinion.

Best,

VB

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Re: [Freesurfer] [EXT] Re: PetSurfer Crashing {Disarmed}

2020-07-20 Thread Crawford, Anna

External Email - Use Caution

My mistake, I think that fixed it.


Thank you!

Anna


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Douglas Greve 

Sent: Monday, July 20, 2020 11:45 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [EXT] Re: [Freesurfer] PetSurfer Crashing

Did you really mean to pass   subject/mri/gtmseg.lta ? The registration is 
supposed to be the registration of the input (PET.template.nii.gz) to the 
anatomical. subject/mri/gtmseg.lta is the registration of gtmseg.mgz to the 
anatomical.

On 7/20/20 11:21 AM, Crawford, Anna wrote:

External Email - Use Caution

Hello,


I am trying to run the PetSurfer process for the first time. I was able to run 
gtmseg and mri_coreg which seemed to go okay. When I tried running mri_gtmpvc, 
it is crashing, but I am not sure why. The command I am using and output are 
below. Do you have any guidance as to what is going wrong?


Thank you,

Anna



mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 
6 --seg subject/mri/gtmseg.mgz  --default-seg-merge --auto-mask PSF .01 --mgx 
.01 --o subject/gtmpvc.output
Loading input ../CTPET/PET.template.nii.gz
  done loading input 1 frames

$Id: mri_gtmpvc.c,v 1.69.2.1 2016/07/08 19:50:25 zkaufman Exp $
setenv SUBJECTS_DIR /mnt/netRAID18/7T/study709/S2sdt/
cd /mnt/autofs/netRAID18/7T/study709/S2sdt
mri_gtmpvc --i ../CTPET/PET.template.nii.gz --reg subject/mri/gtmseg.lta --psf 
6 --seg subject/mri/gtmseg.mgz --default-seg-merge --auto-mask PSF .01 --mgx 
.01 --o subject/gtmpvc.output
sysname  Linux
hostname fmri15
machine  x86_64
user crawforda
vgthresh   0.001000
nReplace   18
0. 0. 0. 0. 0. 0.
20 avail.processors, using 1
Creating output directory subject/gtmpvc.output
Loading seg for gtm subject/mri/gtmseg.mgz
Loading seg ctab subject/mri/gtmseg.ctab
Reading subject/mri/gtmseg.lta
Replacing 18
Pruning ctab
Checking tissue type
done with seg vol
maxFWHM = 2.95567 (voxels), PadThresh=0.0001, nPad=10
Computing auto mask
Automask, reducing FOV
region 256 256 109 reduced to 21 11 3  235 245 106
ERROR: LTAconcat(): LTAs 0 and 1 do not match
LTA 0 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.97615814209e-01 0.000e+00 -8.381903171539307e-09 
-7.62939453125e-06
7.450580596923828e-09 9.98807907104e-01 0.000e+00 
0.000e+00
-7.450580596923828e-09 7.450580596923828e-09 9.98211860657e-01 
-1.52587890625e-05
0.000e+00 0.000e+00 0.000e+00 
9.99403953552e-01
src volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 -2.000e+01
dst volume info
valid = 1  # volume info valid
filename = /mnt/netRAID18/7T/study709/S2sdt//subject/mri/brainmask.mgz
volume = 256 256 256
voxelsize = 1.000e+00 1.000e+00 1.000e+00
xras   = -1.000e+00 0.000e+00 0.000e+00
yras   = 0.000e+00 0.000e+00 -1.000e+00
zras   = 0.000e+00 1.000e+00 0.000e+00
cras   = 4.125e+00 3.554792785644531e+01 -2.000e+01
subject subject
fscale 0.15
LTA 1 ---
type  = 0 # LINEAR_VOX_TO_VOX
nxforms   = 1
mean  = 0. 0. 0.
sigma = 1.
1 4 4
9.99403953552e-01 0.000e+00 0.000e+00 
-2.09237060547e+01
0.000e+00 9.99403953552e-01 0.000e+00 
-1.10762939453e+01
0.000e+00 0.000e+00 1.000e+00 
-3.000e+00
0.000e+00 0.000e+00 0.000e+00 
1.000e+00
src volume info
valid = 1  # volume info valid
filename = ../CTPET/PET.template.nii.gz
volume = 256 256 109
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 0.000e+00
yras   = -0.000e+00 1.000e+00 0.000e+00
zras   = -0.000e+00 -0.000e+00 1.000e+00
cras   = 3.660461425781250e+00 1.723927307128906e+02 1.247645019531250e+03
dst volume info
valid = 1  # volume info valid
filename =
volume = 235 245 106
voxelsize = 2.121269941329956e+00 2.121269941329956e+00 2.02971389771e+00
xras   = -1.000e+00 -0.000e+00 0.000e+00
yras

Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

2020-07-20 Thread Glasser, Matthew

External Email - Use Caution

What is the resolution of these images?

Matt.

From:  on behalf of "Batra, Vinita R." 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 11:13 AM
To: Freesurfer support list 
Subject: [Freesurfer] T2 or FLAIR data to improve pial surfaces

External Email - Use Caution
Dear FreeSurfer experts,

I have both T2 and FLAIR images for the majority of the subjects in my study,
and I want to use them to improve pial surface reconstruction during recon-all
as explained in [1].

My questions are:

1) In general, should I prefer FLAIR over T2, or the other way around?
2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a
T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for 
others, in the same study? We will perform manual QC after the recon-all run 
and exclude bad quality images so I wanted to hear your opinion.

Best,

VB

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 
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immediately notify the sender via telephone or return mail.
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Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

2020-07-20 Thread Batra, Vinita R.

External Email - Use Caution

Equal to that of the T1

From:  on behalf of "Glasser, Matthew" 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 11:42 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

*EXTERNAL EMAIL: EVALUATE*

External Email - Use Caution
What is the resolution of these images?

Matt.

From:  on behalf of "Batra, Vinita R." 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 11:13 AM
To: Freesurfer support list 
Subject: [Freesurfer] T2 or FLAIR data to improve pial surfaces

External Email - Use Caution
Dear FreeSurfer experts,

I have both T2 and FLAIR images for the majority of the subjects in my study,
and I want to use them to improve pial surface reconstruction during recon-all
as explained in [1].

My questions are:

1) In general, should I prefer FLAIR over T2, or the other way around?
2) Some subjects (< 10%) do not have a FLAIR image, and others do not have a
T2. Do you think that it is fine to use FLAIR for some subjects, and T2 for 
others, in the same study? We will perform manual QC after the recon-all run 
and exclude bad quality images so I wanted to hear your opinion.

Best,

VB

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] Error for version 7.1.0 when run the recon-all

2020-07-20 Thread Hoopes, Andrew

Hi Molly,

You might have accidentally passed a non-unicode character to the command line 
(maybe somewhere in the path to the input volume). Sometimes this happens if 
code is copy-pasted from elsewhere. Can you try running it again but manually 
typing out the recon-all command? Otherwise, I’m not quite sure what would be 
going on here.

Best,
Andrew

From:  on behalf of Yang Molly 

Reply-To: FS Help 
Date: Monday, July 20, 2020 at 10:01 AM
To: FS Help 
Subject: [Freesurfer] Error for version 7.1.0 when run the recon-all


External Email - Use Caution

Hi list,

I tried to run the latest version Freesurfer (7.1.0) on the Ubantu 18.04 
system. I downloaded the “freesurfer-linux-centos7_x86_64-7.1.0.tar.gz” and 
successfully installed. I tried to run "recon-all -s bert -autorecon1" and the 
terminal replied as "recon-all -s bert finished without error ". However, when 
I tried to run the recon-all use the common" recon-all -i 
/home/molly/FStry/preA063/preA063.nii -s sub063 -all", the terminal replied

"Traceback (most recent call last):

  File "/usr/local/freesurfer/python/scripts/rca-config", line 137, in 

file.write(arg + '\n')

UnicodeEncodeError: 'ascii' codec can't encode character '\udc87' in position 
12: ordinal not in range(128)

ERROR: could not configure recon-all parameters"

I did not retrieve a similar question in the previous mailing list and hope to 
get your help.

Thank you

Molly

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[Freesurfer] FsAverage4 vertex coordinates

2020-07-20 Thread Walsh, Shane W.

Hi FreeSurfer developers,

I'm looking for the xyz coordinate table for the vertices of the FsAverage4 
atlas. I have fMRI data that has been sampled to the FsAverage4 space and it 
would be helpful if I could understand where a given vertex is located in the 
brain in terms of coordinates. Does anyone on the list know where I could find 
this information? I imagine it may be in the subjects directory that comes with 
the FreeSurfer software, but I haven't been able to locate it.

Thank you for your help,
Shane

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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

2020-07-20 Thread Glasser, Matthew

External Email - Use Caution

wb_command -file-information on the .dlabel.nii file should do the trick.

Matt.

From:  on behalf of Alina Rojas 

Reply-To: Freesurfer support list 
Date: Monday, July 20, 2020 at 6:13 AM
To: Freesurfer support list 
Subject: Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

External Email - Use Caution
Thank you for the quick answer! For the archive and my understanding…the 
pscalar gives out a column with 360 values, these values are the average 
thickness of my one subject and finally, the data I was searching for: cortical 
thickness values from my subject obtained with Freesurfer but with the 
parcellation of the HCP-MMP1. Is there a document or a command where I can 
correlate these values with the name/number of cortical area?

Regards,

Alina

Am 20.07.2020 um 11:32 schrieb Alina Rojas 
mailto:alinacol...@gmail.com>>:

Thank you, the ciftify was run successfully! But now I have questions to the 
wb-command -cifti-parcellate:

wb_command -cifti-parcellate

   - the cifti file to parcellate

   - a cifti label file to use for the parcellation

   - which mapping to parcellate (integer, ROW, or COLUMN)

   - output - output cifti file
I understand that   should be 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii,
 but what should I use as label? The 
Q1-Q6_RelatedParcellation210.L.CorticalAreas_dil_Colors.32k_fs_LR.dlabel.nii 
from https://balsa.wustl.edu/WN56? And the output from the -cifty-parcellate is 
.pscalar.nii..how do I get from there to GIFTI?

And for the GIFTY to .annot I would do:

  mris_convert --annot lh.aparc.gii lh.white.gii lh.aparc.annot (Freesurfer 
example)

Thank you,

Alina

Am 14.07.2020 um 16:17 schrieb Glasser, Matthew 
mailto:glass...@wustl.edu>>:

   External Email - Use Caution

I would find using something like ciftify (https://github.com/edickie/ciftify) 
potentially more straightforward (and then you can just use wb_command 
-cifti-parcellate on 
${StudyFolder}/${Subject}/MNINonLinear/fsaverage_LR32k/${Subject}.thickness.32k_fs_LR.dscalar.nii).
  It is possible to go the other direction too (e.g. using this link: 
https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=&cad=rja&uact=8&ved=2ahUKEwjC2IL-9szqAhWPW80KHb3gAtQQFjACegQIBhAB&url=https%3A%2F%2Fwiki.humanconnectome.org%2Fdownload%2Fattachments%2F63078513%2FResampling-FreeSurfer-HCP_5_8.pdf&usg=AOvVaw0PXEiAKfGjdiN2DJcF7nuI
 and then perhaps someone on the list can explain how to go from GIFTI on 
fsaverage to .annot on the native meshes and extract the stats.

Matt.

On 7/14/20, 8:54 AM, 
"freesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Alina Rojas" 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
 on behalf of alinacol...@gmail.com> wrote:

   * External Email - Caution *

   External Email - Use Caution

   Hello Freesurfer support list,

   I’m attempting to map the HCP-MMP1-Atlas to the individual brains of my 
subjects to get the values of the parcellation, like aparc.stats but aparc 
being HCP-MMP1. The aim ist to compare the cortical thickness of the 
Parcellation given by the HCP-MMP1-Atlas between subjects. I searched the 
archive and didn’t find the solution. It would be so great if you could help me!

   Thank you and regards,

   Alina Rojas

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intended recipient, be advised that any unauthorized use, disclosure, copying 
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strictly prohibited. If you have received this email in error, please 
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[Freesurfer] How to do permutation for multiple comparison correction?

2020-07-20 Thread Xiaojiang Yang

External Email - Use Caution

Dear FS experts,

Instead of using mri_glmfit-sim, I am trying to implement a customized
multiple comparison correction algorithm using permutation. Before I
implement my own, I want to make sure my permutation idea is correct. So I
was looking at how mri_glmfit-sim does the permutation.
The link here
http://freesurfer.net/fswiki/FsTutorial/MultipleComparisonsV6.0Perm has a
simple description for how to do permutation, but I don't quite understand
the 1st step: Permute the design matrix. To me, permute the design matrix
means permute the matrix rows here, but still hard to understand why
permuting matrix rows does the trick.
Anyway, I will not use any design matrix in my customized implementation,
so it does not matter for now.
My problem can be described as follows: if I have a ROI (a label file) on
fsaverage, and I have a test subject and a group of control subjects whose
thickness values on every vertex in this label are all known. (The test
subject and control subjects are all using fsaverage reference space). I
want to compare this test subject's thickness within the ROI to a control
group of subjects (within the same ROI). This is a multiple-comparison
problem, so I want to use permutation to get less FP rate.
My question is: How do I permute the test subject's points and control
subjects' points in ROI?
My understanding is that: for each point in the label, I randomly re-assign
all (1+n) values from (1+n) subjects to these (n+1) subjects (where n is
the number of subjects in control group). And when all points in the label
are done, this is only 1 permutation. I will need at least 1000 times of
permutation to get the comparison statistics.
Is my understanding right?
Thank you!
Xiao
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Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

[Freesurfer] Error for version 7.1.0 when run the recon-all

[Freesurfer] Flag(s) for parallel processing

[Freesurfer] PetSurfer Crashing

Re: [Freesurfer] Right and left on MRI scan and on images

Re: [Freesurfer] Fwd: One hemisphere recon-all ERROR

Re: [Freesurfer] PetSurfer Crashing

[Freesurfer] T2 or FLAIR data to improve pial surfaces

Re: [Freesurfer] [EXT] Re: PetSurfer Crashing {Disarmed}

Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

Re: [Freesurfer] T2 or FLAIR data to improve pial surfaces

Re: [Freesurfer] Error for version 7.1.0 when run the recon-all

[Freesurfer] FsAverage4 vertex coordinates

Re: [Freesurfer] HCP-MMP1 Parcellation to individual brain for stats

[Freesurfer] How to do permutation for multiple comparison correction?

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