[Freesurfer] No ROI name in summary of MNI305 group analysis

[wangzhiwei3233]

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Dear Freesurfer Experts,
I did group-level analysis in MNI305 space.  Then I output the summay via 
command 'mri_volcluster' as follows:
mri_volcluster --in ./sig.nii.gz  --thmin ${thvoxel} --sign ${sigsignTemp} 
--cwpvalthresh 0.05 --minsize 273 --fwhm 6--no-adjust --sum 
${nameout}.cluster.summary --out ${nameout}.cluster.nii.gz --ocn 
${nameout}.ocn.nii.gz --labelbase 
$Dir_Subj_fMRI/$out_dir_group/$analysis/$contrast/label_${nameout}/label --mask 
/mnt/hgfs/G/work/MetaCog/Human/subjects/fsaverage/mri.2mm/subcort.mask.mgz


the output is as follows. there are no ROI names in the table. Is it because I 
missed the option '--reg' in the command line? Which register file shoul I use 
if I should add it? I can't find the 'register.dat' file in fsaverage folder. 


Very appricated if you can help me. 


Best,
zhiwei 
-

# Reporting Coordinates in Voxel Indices
# Cluster   Size(n)   Size(mm^3) VoxXVoxYVoxZ Max 
GRFCWP
  1 5270   42160.0  33.00   35.00   60.00   6.04524  
0.001
  2 1995   15960.0  15.00   65.00   24.00   4.32869  
0.0008543
  3 1429   11432.0  51.00   64.00   17.00   3.72032  
0.0036314
  4  6905520.0  55.00   56.00   49.00  -3.22358  
0.0488862

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[Freesurfer] vol2subfield troubleshoot

[Mirsol Choi]

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Hello Freesurfers,

My name is Mirsol and I am currently trying to obtain FA values from
particular hippocampus subfields by registering our fractional anisotropy
map (FA.nii.gz) from dt_recon command and our hippocampus segmentations
from the command segmentHA_T1.sh.

I have followed the protocol on the website "Segmentation of hippocampal
subfields and nuclei of the amygdala" to perform the segmentation, and at
the bottom of the website, it mentions:
"6. Multimodal integration

To extract values within the subfields from another modality (eg, DTI or
fMRI), use vol2subfield. Run with --help for examples."


Upon using vol2subfield --help on UNIX (macOS), I was shown these scripts:


1. To get a registration between an input volume and a subfield volume


vol2subfield --i fa.nii.gz --reg reg.lta --sf
rh.hippoAmygLabels-T1.v22.HBT.mgz --outreg outreg.lta


2. To map the input volume into the subfield volume space


vol2subfield --i fa.nii.gz --reg reg.lta --sf
rh.hippoAmygLabels-T1.v22.HBT.mgz --o fa.rh.hbt.mgz




3. To compute segmentation statistics of the input volume


vol2subfield --i fa.nii.gz --reg reg.lta --sf
rh.hippoAmygLabels-T1.v22.HBT.mgz \

  --o fa.rh.hbt.mgz --stats stats.dat --avgwf avgwf.dat --avgwfvol
avgwfvol.mgz



I have tried all three codes presented here, but I am met with this message
when I do.


"set: Variable name must contain alphanumeric characters."



I am quite unsure what to do from here and have not been able to
troubleshoot this issue.


If someone out there could offer some advice or support, I will be forever
grateful.


Thank you so much for your time,

Mirsol
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[Freesurfer] Late applications due by Nov 30th: NIH R25 Course Training in Advancd Statistical Methods in Neuroimaging and Genetics, Salt Lake City, Utah, April 15-26, 2024.

[ROBERT CARY WELSH]

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Hi everybody,
We are pleased to announce that the application portal is still open for the 
NIH funded 2024 session of the course, “Training in Advanced Statistical 
Methods in Neuroimaging and Genetics”.

We hope you pass this email on to your local neuroimaging community.

The course will start on Monday, April 15, 2024 and finish on April 26, 2024 
and is to be held in person, in Salt Lake City, Utah, United States at the 
University Guest House Conference Center. Our course also includes an ongoing 
(throughout the year) continuing education portion.

The course is an intensive 2-weeks, about 8 hours per day of a mix of lectures 
and hands-on computer labs.

neurostatsbootcamp.org

Due to recently increased funding, we are pleased to announce we can drop our 
tuition this year to $2250. Strictly financial need scholarships will also 
still be offered.

Tuition includes hotel accommodations at the University Guest House (arrival on 
April 14 with departure on April 26), breakfast, lunch, day time snacks, three 
dinners out as a group, and the planned evening activities. All course 
attendees will arrange for their own transportation to Salt Lake City. The 
course cost does include a daily pass to the Salt Lake City Trax light 
rail/commuter system. (Please note that the course instructors' effort is 
supported by the NIH grant thus avoiding that cost being passed on to the 
course attendees. This course is strictly not-for-profit.)
Because of the limited size and advanced nature of the course, attendance is by 
application only – please make sure to fully read the website instructions. In 
general, applicants must be a US citizen, permanent resident, or working with 
an appointment at a US institution, though we do have the ability to 
accommodate 3 to 6 individuals that do not meet this criteria. We anticipate 
the total class size to be between 22 and 25 students.

There are opportunities for scholarships which can partially offset hotel 
accommodations. These are based on true financial need and you will be 
instructed how to apply if you are admitted to the course.

We look forward to seeing you in SLC in 2024!

Late application deadline is Dec 1, 2023; decisions by Jan 5th, 2024.

For more information email us at 
neurost...@g.ucla.edu (or 
advancedstatisticscou...@utah.edu)

Robert and Anna

--
Robert Welsh, PhD
Course Director, Training in Advanced Statistical Methods in Neuroimaging and 
Genetics
rcwe...@g.ucla.edu
robert.c.we...@utah.edu

Anna Docherty, PhD
Associate Course Director, Training in Advanced Statistical Methods in 
Neuroimaging and Genetics
anna.doche...@utah.edu

Christina Caldera
Course Administrator
neurost...@g.ucla.edu

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[Freesurfer] Errors in LGI command

[笹林大樹]

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Dear Freesurfer experts,

I have run the following command:
recon-all -s sub-1001 -localGI -no-isrunning

However, I got the error message as below.

>> Warning: Input argument must be a character vector.  
> In ver (line 41) In freesurfer_read_surf (line 70) In 
> find_corresponding_center_FSformat (line 26)  
Error using fprintf 
Function is not defined for 'struct' inputs.  

Error in freesurfer_read_surf (line 70) 
fprintf('FREESURFER_READ_SURF [v %s]\n',ver(11:15));  

Error in find_corresponding_center_FSformat (line 26) 
[mesh_pial.vertices, mesh_pial.faces] = freesurfer_read_surf(pial);  

>>  
ERROR: find_corresponding_center_FSformat did not complete successfully! Linux 
dn003 3.10.0-1160.88.1.el7.x86_64 #1 SMP Tue Mar 7 15:41:52 UTC 2023 x86_64 
x86_64 x86_64 GNU/Linux  

recon-all -s sub-1001 exited with ERRORS at Wed Nov 22 14:59:33 EST 2023

How can I resolve the problem?
Thank you for your consideration.

Best,

Daiki Sasabayashi___
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Re: [Freesurfer] About Mean LGI value

[笹林大樹]

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Dear Dr. Greve,

Thank you for your answer!
I found this helpful.

Best,
Daiki Sasabayashi

> 2023/11/22 13:06、Douglas N. Greve のメール:
> 
> If the difference is only between 3.0761 and 3.0327, then that is acceptably 
> small to disregard.
> 
> On 11/21/2023 10:40 AM, 笹林大樹 wrote:
>> External Email - Use Caution
>> 
>> Dear Dr. Greve,
>> 
>> I trust this message finds you well. I wanted to follow up on the inquiry I 
>> posted to the FreeSurfer mailing list a while back regarding "About Mean LGI 
>> value" as below.
>> I understand you are busy, and I appreciate your dedication to the 
>> community. If possible, could you revisit my query when time permits?
>> Thank you for your time, and I look forward to hearing from you.
>> 
>> 
>> Best,
>> 
>> Daiki Sasabayashi
>> 
>> 
>> 
>>> 転送されたメッセージ:
>>> 
>>> 差出人: 笹林大樹 mailto:ds...@med.u-toyama.ac.jp>>
>>> 件名: Re: [Freesurfer] About Mean LGI value
>>> 日付: 2023年11月9日 10:37:38 GMT-5
>>> 宛先: Freesurfer support list >> >
>>> 返信先: Freesurfer support list >> >
>>> 
>>> External Email - Use Caution
>>> 
>>> 
>>> Dear. Dr. Greve,
>>> 
>>> Thank you for your response.
>>> I attached both “*h.aparc.pial_lgi.stats” and 
>>> “*h.aparc.mean_pial_lgi.stats” files.
>>> For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, 
>>> Seg0001, is it correct as mean LGI value?), while the average of the LGI 
>>> values is about 3.0327 (the sum of the LGI values of the 34 DK atlas ROIs 
>>> divided by 34: value calculated here).
>>> Are these values acceptable?
>>> 
>>> Daiki Sasabayashi
>>> 
>> 
>> 
>> 
>> 
>>> 
 2023/11/09 9:33、Douglas N. Greve >>> >のメール:
 
 How different are the values? Those two stats files are created with 
 different programs, so there could be some small differences. But if 
 you're seeing large differences, then that is something else. If the 
 latter, then send both stats files.
 
 On 11/3/2023 9:14 AM, 笹林大樹 wrote:
> External Email - Use Caution
> 
> Dear Freesurfer experts,
> 
> I have calculated the mean LGI value for each hemisphere by referring to 
> previous archives below. 
> However, this mean LGI value differs from the average of the LGI values 
> listed in *h/aparc.pial_lgi.stats (i.e., the sum of the LGI values of the 
> 34 DK atlas ROIs divided by 34). 
> Are these values originally subject to discrepancy?
> 
> Best,
> 
> Daiki Sasabayashi
> 
> Re: [Freesurfer] Mean Gyrification index 
> 
> Dougla s N. Greve 
> 
>  Wed, 09 Sep 2020 08:26:32 -0700 
> 
> It is giving you values for two segmentations: inside the label and 
> outside the label. Use --id 1 to get only values inside the cortex label
> On 9/9/2020 11:27 AM, vittal korann wrote:
> External Email - Use Caution
> 
> Dear FreeSurfer experts
> 
> I am working on the gyrification index of schizophrenia patients. I had 
> collated global brain values such as thickness, GM, and WM volumes. In 
> addition, I wanted to tabulate gyrification values. Using the below link 
> I was able to extract the hemispheric mean gyrification values.
> MailScanner has detected a possible fraud attempt from 
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Re: [Freesurfer] Question about lesions output of samseg

[Koen Van Leemput]

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Hi Reza,

The lesion class in samseg is a bit special, as the internal lesion
probabilities are thresholded (using the value passed on via the
--threshold flag, or a default value 0.3 if you didn't use that flag) to
obtain the voxels labeled as 99 in the segmentation output. In contrast,
the value in the .stats file is simply the sum (over all voxels) of those
internal lesion probabilities.

If you want to inspect the impact of the exact threshold value on the
number of voxels with label 99, you could run samseg with the
--save-posteriors flag to save the internal lesion probabilities (in
yourSeg/posteriors/Lesions.mgz). Then you can play with mri_binarize and
mri_segstats to obtain lesion volumes for different thresholds without
having to re-run sameg anew.

Hope this helps,

Koen


On Thu, Nov 16, 2023 at 9:45 AM reza razmara  wrote:

> External Email - Use Caution
>
> Thanks
>
> The volume of lesions in label 99 in seg.mgz result is 745 mm^3.
>
> The samseg output for lesions in samseg.stats is 633 mm^3.
> Is it ok?
>
> On Thu, Nov 16, 2023, 5:57 PM Douglas N. Greve 
> wrote:
>
>> Internally, samseg uses partial volume to compute a more accurate volume.
>> They should still be very close though.
>>
>> On 11/16/2023 6:46 AM, reza razmara wrote:
>>
>> External Email - Use Caution
>> Hi freesurfer team
>>
>> I use samseg for lesion segmentation. In the result of .stats i see the
>> lesions volume. But when i extract lesions seprately as a new file we know
>> that it uses the label 99 for extraction. But when i calculate the volume
>> of this extracted lesions which i created it seprately. The volume of these
>> two results are not the same.
>> The volume of extracted lesions seprately is higher than what samseg
>> automatically calculated in .stats file.
>> Why is this happened? Why the volumes are not the same. And how can i
>> calculate the lesions volume from extracted file that i created which is a
>> flair that i masked with label 99? How can i recalculate the lesions volume
>> from just exracted lesions filr without using samseg?
>>
>> Thanks a lot for your help
>>
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>>
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Re: [Freesurfer] issue with mri_vol2surf

[Atena Akbari]

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[image: Screenshot 2023-11-22 at 1.32.53 PM.png]
 doesn't allow me to adjust the threshold to negative values, for example
t-values between -3 and 3.

On Wed, Nov 22, 2023 at 1:26 PM Douglas N. Greve 
wrote:

> Have you tried adjusting the threshold. Open the configure overlay option.
> Also, sending a pic would be helpful (and the contents of tk.dat)
>
> On 11/22/2023 11:29 AM, Atena Akbari wrote:
>
> External Email - Use Caution
> Dear freesurfer team,
>
> I want to overlay the activation map that I got from SPM on the inflated
> surface. The command I use is:
>
>
> "mri_vol2surf--mov spmT_funcmap.nii --ref
>  subj01/mri/orig.mgz.   --regtk.dat--hemi rh   --oflodername"
>
>
> in which, I got the registration file (tk.dat) by aligning my
> functional mean image to the orig.mgz in tkregisterfv.
>
>
> now the problem is when I overlay the activation map on the inflated
> surface, I can only see the voxels with positive t-values. I can't see the
> negative ones. I cannot change the threshold values provided by "configure
> overlay" to negative values. Also, changing the "z-score" option next to
> the overlay configuration doesn't make any difference. can you help me with
> this, please?
>
>
> Thanks a lot,
>
> Atena
>
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tk2.dat
Description: Binary data
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Re: [Freesurfer] issue with mri_vol2surf

[Douglas N. Greve]

Have you tried adjusting the threshold. Open the configure overlay 
option. Also, sending a pic would be helpful (and the contents of tk.dat)


On 11/22/2023 11:29 AM, Atena Akbari wrote:


External Email - Use Caution

Dear freesurfer team,

I want to overlay the activation map that I got from SPM on the 
inflated surface. The command I use is:



"mri_vol2surf    --mov  spmT_funcmap.nii     --ref    
 subj01/mri/orig.mgz.  --reg    tk.dat    --hemi rh   --o    flodername"



in which, I got the registration file (tk.dat) by aligning my 
functional mean image to the orig.mgz in tkregisterfv.



now the problem is when I overlay the activation map on the inflated 
surface, I can only see the voxels with positive t-values. I can't see 
the negative ones. I cannot change the threshold values provided by 
"configure overlay" to negative values. Also, changing the "z-score" 
option next to the overlay configuration doesn't make any difference. 
can you help me with this, please?



Thanks a lot,

Atena


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 .
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Re: [Freesurfer] Boundary based registration on partial FoV to MNI space

[Douglas N. Greve]

You are not going to be able to register the partial FoV directly to 
mni152. You can register the partial FoV to a full FoV within subject 
and then the full FoV to mni152, then concatenate the registrations 
together.


On 11/22/2023 8:01 AM, Spapens, Jeltje (NP) wrote:


External Email - Use Caution

Hi Douglas,

Thank you for your feedback. I registered the anatomical T1 scan 
(output recon-all) to the MNI image with FLIRT (MRS_101_FLIRT.nii). 
So, I decided to register the partial FoV scan 
(MRS_101_MT_tfl_stripped.nii) to the MRS_101_FLIRT.nii.


I tried both bbregister and mricoreg, but both did not work. The 
bbregister output had an oblique output and was registered to the 
wrong image. The mri_coreg did not correctly register as seen in the 
screenshot.


I used following commands:

*bbregister*

bbregister --s MRS_101_recon_all --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.nii 
--reg MRS_101_NM2mp2rage.dat --t2 --init-header


mri_vol2vol--mov/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.nii 
--targ 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_FLIRT.nii 
--o 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_regt1.nii.gz 
--reg MRS_101_NM2mp2rage.dat –cubic


*mri_coreg*

mri_coreg --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.mgz 
--targ 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_FLIRT.nii 
--reg 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_coregistration.lta


mri_vol2vol --mov 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_MT_tfl_stripped.mgz 
--targ 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_FLIRT.nii 
--reg 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_coregistration.lta 
--o 
/Users/robspapens/Desktop/Thesis/Subjects/MRS_101/MRS_101_coregistered.mgz


Kind regards,

Jeltje Spapens

*From: * on behalf of "Douglas 
N. Greve" 

*Reply to: *Freesurfer support list 
*Date: *Tuesday, 21 November 2023 at 18.31
*To: *"freesurfer@nmr.mgh.harvard.edu" 
*Subject: *Re: [Freesurfer] Boundary based registration on partial FoV 
to MNI space


Is MRS_201_MT_tfl_stripped.mgz  correctly oriented when  you view it 
in freeview? Also, bbr is meant to be used for within subject 
registration. For something like registering to the mni152, try 
mri_coreg and specify --dof 12


On 11/20/2023 10:00 AM, Spapens, Jeltje (NP) wrote:

*External Email - Use Caution *

Hello Freesurfer developers.

I tried the boundary-based registration of a partial FoV to a MNI
space template with the following two step code:

bbregister --s MRS_201_recon_all --mov

/Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz
--reg MRS_201_NM2mp2rage.dat --t2 --init-header

mri_vol2vol--mov

/Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_stripped.mgz
--targ /Users/robspapens/Desktop/Thesis/Subjects/MNI_upsamp.nii
--o

/Users/robspapens/Desktop/Thesis/Subjects/MRS_201/MRS_201_MT_tfl_regt1.nii.gz
--reg MRS_201_NM2mp2rage.dat --cubic

When I open the scan in Freeview or FSLeyes the orientation is not
correct. The Horizontal plane is labeled as the Coronal plane and
the sagittal plane is rotated 90 degrees.

I tried: fslreorient2std input_file.nii.gz output_file.nii.gz, but
this gave the same result. I also tried it on 3 scans and all give
the same wrong orientation after the BBR.

How can I best register the scan with small FoV to the MNI space
template?

With kind regards,

Jeltje Spapens



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Re: [Freesurfer] recon-all error - MRISlabel2Mask()

[Douglas N. Greve]

yes, sending the full log file will be helpful. My guess is that the 
surfaces got out of synch (eg, if you had done edits).


On 11/21/2023 8:15 PM, Mark Wagshul wrote:


External Email - Use Caution

Dear Freesurfer experts,

Hi. Hoping someone can give me some guidance in how to proceed with 
this error in recon-all (at the moment, was running autorecon-wm, but 
not sure that’s relevant). Just pasting the last few commands which 
were successfully run, can send the whole recon-all.log file if 
needed. Nothing obvious in terms of the T1 or T2 images. Thanks!


#===

mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg 
--surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz 
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf


Reading header for orig.mgz

Source registration surface changed to woT2.pial.rawavg

Target registration surface changed to woT2.pial.rawavg

7.3.2

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w


cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


mri_surf2surf --s sub-XXX --hemi rh --sval-xyz woT2.pial.rawavg 
--surfreg woT2.pial.rawavg --reg transforms/conf2rawavg.dat orig.mgz 
--tval-xyz orig.mgz --tval woT2.pial.rawavg.conf


sysname  Linux

hostname cpu-771.cluster.local

machine  x86_64

user mwagshul

srcsubject = sub-XXX

srcval = (null)

srctype    =

trgsubject = sub-XXX

trgval = woT2.pial.rawavg.conf

trgtype    =

srcsurfreg = woT2.pial.rawavg

trgsurfreg = woT2.pial.rawavg

srchemi    = rh

trghemi    = rh

frame  = 0

fwhm-in    = 0

fwhm-out   = 0

label-src  = (null)

label-trg  = (null)

OKToRevFaceOrder = 1

UseDualHemi = 0

Reading source surface reg 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg


Loading source data

Reading surface file 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf/rh.woT2.pial.rawavg


Applying linear registration transform

1.0 0.0   0.0  -0.4;

0.0 1.0   0.0   0.0;

0.0 0.0   1.0   0.3;

0.0 0.0   0.0   1.0;

INFO: trgsubject = srcsubject

Saving target data

/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/surf 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri 



/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri 



Tue Nov 21 17:49:18 EST 2023

#===

bbregister --s sub-XXX --mov orig/T2raw.mgz --lta 
transforms/T2raw.auto.lta --init-coreg --t2 --surf white.preaparc 
--proj-abs 1.5 --threads 1


tmp transforms/tmp.bbregister.3166191

Log file is transforms/T2raw.auto.log

Tue Nov 21 17:49:18 EST 2023

setenv SUBJECTS_DIR 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w


cd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


/public/apps/freesurfer/7.3.2/bin/bbregister --s sub-XXX --mov 
orig/T2raw.mgz --lta transforms/T2raw.auto.lta --init-coreg --t2 
--surf white.preaparc --proj-abs 1.5 --threads 1


bbregister 7.3.2

Linux cpu-771.cluster.local 4.18.0-477.13.1.el8_8.x86_64 #1 SMP Thu 
May 18 10:27:05 EDT 2023 x86_64 x86_64 x86_64 GNU/Linux


FREESURFER_HOME /public/apps/freesurfer/7.3.2

mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii

mri_convert orig/T2raw.mgz transforms/tmp.bbregister.3166191/template.nii

reading from orig/T2raw.mgz...

TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (-1, 0, 0)

j_ras = (0, 1, 0)

k_ras = (0, 0, 1)

writing to transforms/tmp.bbregister.3166191/template.nii...

mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 
--sep 4 --ftol .0001 --linmintol .01


$Id: mri_coreg.c,v 1.27 2016/04/30 15:11:49 greve Exp $

cwd 
/gs/gsfs0/shared-dept/mrrc-all/PROJECTS/P80-ADT/BIDS/hcp_output/sub-XXX/T1w/sub-XXX/mri


cmdline mri_coreg --s sub-XXX --mov 
transforms/tmp.bbregister.3166191/template.nii --regdat 
transforms/tmp.bbregister.3166191/reg.init.dat --reg 
transforms/tmp.bbregister.3166191/mri_coreg.lta --nthreads 1 --dof 6 
--sep 4 --ftol .0001 --linmintol .01


sysname  Linux

hostname cpu-771.cluster.local

machine  x86_64

user mwagshul

dof    6

nsep    1

cras0    1

ftol    0.000100

linmintol 0.01

bf   1

bflim 30.00

bfnsamp    30

SmoothRef 0

SatPct 99.99

MovOOB 0

optschema 1

Seed 53

Reading in mov transforms/tmp.bbregister.3166191/template.nii

Reading in ref brainmask.mgz

Reading in and applying refmask aparc+aseg.mgz

Setting cras translation parameters to align volume centers

Creating random numbers for coordinate dithering

Performing intensity 

Re: [Freesurfer] Distance Measurement After recon-all

[Douglas N. Greve]

You can use mri_vol2surf, something like
mri_vol2surf --closest-vertex x y z coords ltafile surf outfile
where xyz is a coordinate (eg, the center or edge or you lesion).
coords: 1=scanner,2=tkreg (you can pick the xyz from the freeview 
scanner or tkreg ras)
if these coordinates are in the same space as the anatomical (ie, 
conformed, 1mm, 256^3), then set ltafile to nofile

surf is the surface file (eg, lh.white)
The outfile will have the vertex number of the closest vertex.

On 11/21/2023 12:49 PM, John Anderson wrote:


External Email - Use Caution

Dear Freesurfer Experts,
I would like to inquire if there is a FreeSurfer command that allows 
me to measure the distance (in voxels or mm) between a lesion mask 
(output of samseg) and the closest voxels in the ribbon after applying 
"recon-all" to T1 images. If there is no such command, I am 
considering measuring the center of the lesion mask and calculating 
the distance between this center and every voxel in the closest parcel 
in the ribbon, then selecting the shortest distance. i'm not sure if 
this is the correct approach so I appreciate your suggestions.

Thank you
John

On Mon, Nov 20, 2023 at 7:13 AM John Anderson  
wrote:


Dear FreeSurfer experts, I would like to know if there is a
command in FreeSurfer that can help me measure the distance (in
voxels or mm) between a lesion mask and the closest voxels in the
ribbon after applying recon-all to T1 images. Thanks for your advice

John


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Re: [Freesurfer] Transformation of volume images

[Douglas N. Greve]

You can use  something like
mri_convert orig.mgz -at mri/talairach.m3z orig-in-mni305.mgz
This is nonlinear. It takes you to the mni305 space.

On 11/21/2023 11:45 AM, P Pieperhoff wrote:


External Email - Use Caution

Hi Yujing,
thank you for your help! But I think, this is only the affine 
registration?
Is it possible that I can use the same transformation, by which e.g. 
aseg.mgz-atlas is transformed into the native space of a given subject?
The volume-dataset of the subcortical regions matches quite well with 
the subcortical structure of each subject, but I think that this can't 
be achieved by an affine transformation only.


Best regards,
Peter




On Fri, Nov 17, 2023 at 3:57 PM Huang, Yujing 
 wrote:


Hi Peter,

Here is an example to convert from native space to MNI305
(fsaverage) in *MailScanner has detected a possible fraud attempt
from "secure-web.cisco.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/mri_vol2vol



  mri_vol2vol --mov orig.mgz

 --targ $FREESURFER_HOME/average/mni305.cor.mgz

 --xfm transforms/talairach.xfm

 --o orig-in-mni305.mgz

In your case, I think you also need ‘—interp nearest’ to convert
segmentation.

To convert from fsaverage to native space of a subject, can you
try the following? I used bert as an example.

 mri_vol2vol

   --mov bert/mri/orig.mgz

   --targ fsaverage/mri/aseg.mgz

   --xfm transforms/talairach.xfm

   --inv

   --o aseg-from-mni305.mgz

   --interp nearest

Best,

Yujing

*From:* freesurfer-boun...@nmr.mgh.harvard.edu
 *On Behalf Of *P Pieperhoff
*Sent:* Thursday, November 16, 2023 12:07 PM
*To:* Freesurfer support list 
*Subject:* [Freesurfer] Transformation of volume images

*External Email - Use Caution *

Dear developers,

please, may I ask you how I can transform volume images
(containing discrete region labels) from the fsaverage space into
the space of a given subject, and vice-versa?

I tried the following command:

mri_vol2vol --interp nearest --mov fsaverage/mri/aseg.mgz  --o
test_mask.mgz    --s test001  --targ test001/mri/orig.mg



or

mri_vol2vol   --interp nearest --mov fsaverage/mri/aseg.mgz  --o
test_mask.mgz    --targ  test001/mri/T1.mgz  --lta
 test001/mri/transforms/talairach.lta --m3z talairach.m3z
--s test001

but there was always a large mismatch between the transformed
images and the target image.

Best regards,

Peter

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Re: [Freesurfer] Fwd: About Mean LGI value

[Douglas N. Greve]

If the difference is only between 3.0761 and 3.0327, then that is 
acceptably small to disregard.


On 11/21/2023 10:40 AM, 笹林大樹 wrote:


External Email - Use Caution

Dear Dr. Greve,

I trust this message finds you well. I wanted to follow up on the 
inquiry I posted to the FreeSurfer mailing list a while back regarding 
"About Mean LGI value" as below.
I understand you are busy, and I appreciate your dedication to the 
community. If possible, could you revisit my query when time permits?

Thank you for your time, and I look forward to hearing from you.

Best,
Daiki Sasabayashi

転送されたメッセージ:

*差出人: *笹林大樹 
*件名: **Re: [Freesurfer] About Mean LGI value*
*日付: *2023年11月9日 10:37:38 GMT-5
*宛先: *Freesurfer support list 
*返信先: *Freesurfer support list 

External Email - Use Caution


Dear. Dr. Greve,

Thank you for your response.
I attached both “*h.aparc.pial_lgi.stats” and 
“*h.aparc.mean_pial_lgi.stats” files.
For example, in left hemisphere, mean LGI value is 3.0761 (SegId 1, 
Seg0001, is it correct as mean LGI value?), while the average of the 
LGI values is about 3.0327 (the sum of the LGI values of the 34 DK 
atlas ROIs divided by 34: value calculated here).

Are these values acceptable?

Daiki Sasabayashi



2023/11/09 9:33、Douglas N. Greve のメール:

How different are the values? Those two stats files are created with 
different programs, so there could be some small differences. But if 
you're seeing large differences, then that is something else. If the 
latter, then send both stats files.


On 11/3/2023 9:14 AM, 笹林大樹 wrote:


External Email - Use Caution

Dear Freesurfer experts,

I have calculated the mean LGI value for each hemisphere by 
referring to previous archives below.
However, this mean LGI value differs from the average of the LGI 
values listed in *h/aparc.pial_lgi.stats (i.e., the sum of the LGI 
values of the 34 DK atlas ROIs divided by 34).

Are these values originally subject to discrepancy?

Best,

Daiki Sasabayashi


  Re: [Freesurfer] Mean Gyrification index
  


Dougla s N. Greve 
 
Wed, 09 Sep 2020 08:26:32 -0700 



It is giving you values for two segmentations: inside the label and 
outside the label. Use --id 1 to get only values inside the cortex 
label

On 9/9/2020 11:27 AM, vittal korann wrote:

 External Email - Use Caution

Dear FreeSurfer experts

I am working on the gyrification index of schizophrenia
patients. I had collated global brain values such as thickness,
GM, and WM volumes. In addition, I wanted to tabulate
gyrification values. Using the below link I was able to extract
the hemispheric mean gyrification values.

*MailScanner has detected a possible fraud attempt from
"secure-web.cisco.com" claiming to be*
https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg31829.html  


But it is giving me 2 rows of output that are adding more
ambiguity to the existing problem. Below is the command which I
used to get mean gyrification for the left hemisphere and also
the corresponding output.

Re: [Freesurfer] total intracranial volume

[Douglas N. Greve]

They are not

On 11/20/2023 6:01 AM, yunus soleymani wrote:


External Email - Use Caution

Hi Freesurfers,
I wanted to know if the Freesurfer volume results are already 
normalized by the total intracranial volume or if I should normalize 
it for each subject myself.

Thanks for your answer,
Yunus


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Re: [Freesurfer] run recon-all with already skull-stripped data

[Douglas N. Greve]

did you look at the results (eg, the aseg)? Can you send the 
recon-all.log file?



On 11/19/2023 11:18 PM, June Kang wrote:


External Email - Use Caution

Hello,


According to the FAQ for earlier version of Freesurfer (maybe 6.x), 
the instruction is below.



First you must run only -autorecon1 like this:
*recon-all -autorecon1 -noskullstrip -s *

Then you will have to make a symbolic link or copy T1.mgz to 
brainmask.auto.mgz and a link from brainmask.auto.mgz to 
brainmask.mgz. Finally, open this brainmask.mgz file and check that it 
looks okay (there is no skull, cerebellum is intact; use the sample 
subject *bert* that comes with your FreeSurfer installation to make 
sure it looks comparable). From there you can run the final stages of 
recon-all:

*recon-all -autrecon2 -autorecon3 -s *


The autorecon1 step works good, however, second step ends with error 
repeatedly in 7.4.1



516 voxels in left wm, 1068 in right wm, xrange [124, 129]

searching rotation angles z=[-7  7], y=[83 97]

searching scale 1 Z rot 6.8  global minimum found at slice 0.0, 
rotations (90.00, -0.00)


final transformation (x=0.0, yr=90.000, zr=-0.000):

-0.0   0.0   1.0   128.0;

 0.0   1.0   0.0   128.0;

-1.0   0.0  -0.0   127.9;

 0.0   0.0   0.0   1.0;

error: No such file or directory

error: mri_cc: no WM voxels found with norm > 40 -- check skull stripping


Bests,

J.


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Re: [Freesurfer] Unable to add FGATIR during thalamic segmentation

[Iglesias Gonzalez, Juan E.]

Dear Amrita,
Please insert your subject directory between your subject name(sub-19253779) 
and your FGATIR scan (sub-19253779/mri/FGATIR.nii.gz).
If you running your code from the subjects directory, which seems to be the 
case, it would simply be:
segmentThalamicNuclei.sh sub-19253779 .  sub-19253779/mri/FGATIR.nii.gz FGATIR 
t2
Cheers,
/E

--
Juan Eugenio Iglesias
http://www.jeiglesias.com

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Pal, Amrita 

Date: Wednesday, November 22, 2023 at 10:25
To: freesurfer@nmr.mgh.harvard.edu 
Subject: [Freesurfer] Unable to add FGATIR during thalamic segmentation

External Email - Use Caution
Hi

I am unable to add an additional scan FGATIR during thalamic segmentation. For 
example I have a subject in the freesurfer/subjects directory that does 
thalamic segmentation without adding the additional scan but not with the 
attached code. I tried different flags but that didn’t work. Can you please 
help?
[cid:image001.png@01DA1D2E.1672BBD0]
Thanks
Regards
Amrita

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[Freesurfer] issue with mri_vol2surf

[Atena Akbari]

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Dear freesurfer team,

I want to overlay the activation map that I got from SPM on the inflated
surface. The command I use is:


"mri_vol2surf--mov spmT_funcmap.nii --ref
 subj01/mri/orig.mgz.   --regtk.dat--hemi rh   --oflodername"


in which, I got the registration file (tk.dat) by aligning my
functional mean image to the orig.mgz in tkregisterfv.


now the problem is when I overlay the activation map on the inflated
surface, I can only see the voxels with positive t-values. I can't see the
negative ones. I cannot change the threshold values provided by "configure
overlay" to negative values. Also, changing the "z-score" option next to
the overlay configuration doesn't make any difference. can you help me with
this, please?


Thanks a lot,

Atena
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[Freesurfer] Unable to add FGATIR during thalamic segmentation

[Pal, Amrita]

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Hi

I am unable to add an additional scan FGATIR during thalamic segmentation. For 
example I have a subject in the freesurfer/subjects directory that does 
thalamic segmentation without adding the additional scan but not with the 
attached code. I tried different flags but that didn't work. Can you please 
help?
[cid:image001.png@01DA1D2E.1672BBD0]
Thanks
Regards
Amrita

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Re: [Freesurfer] freesurfer results QC

[yunus soleymani]

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Thanks a lot Kersten


 

On Wednesday, November 22, 2023 at 02:04:33 PM GMT+3:30, Diers, Kersten 
/DZNE  wrote:  
 
 
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Hi Yununs,
thanks for your mail:
There are no fixed and hard thresholds for these metrics (e.g., SNR). It really 
depends on the sample and image characteristics. More important than the 
absolute values is the distribution of these values across cases; that is, we 
typically use them to check if are there any images that have very different 
values than the others (outliers). These images would then require closer 
inspection.
Best,
Kersten
On Sun, 2023-11-19 at 07:47 +, yunus soleymani wrote:


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Hi Freesurfer users,
I have recently used the FSQC algorithm 
(https://secure-web.cisco.com/1vSf3_saryaQtzDMCTPgjMgeK-DIgzTXVXy-u7vffEbhTytd47ek-Bmud99Miu1rr0WPuR3yPj-TCe9VJfQ6g-aUJU_QSs8tPG8IprgWdycC4rDDH9VqOR-F32kQwmE0aPWDdzjQRvZB0ouoc11eVPTTMe_Q6ukJqIMoaejF1CUCHFPJLR2ynP0NiXIqilfqxt3NTkpR2N22jaPBHKLmEnIVFgtQtfQDh1OB9ozqp9ObWwhaNHFzcwzOn4Bs0pTn5-IS9iiEqcLkF0ZSE55kkT6opxE9SjpJvUhq7--L3P3yEvxc4vkjaE35xflh-UHlnPEZGjHcrjCsp6Sppi2nYQA/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc%23usage)
 to check the quality of my Freesurfer volumetric results. However, I am having 
trouble understanding the meaning of the output numbers. What is the acceptable 
threshold number of SNR? I would appreciate any help you can provide.
Thank you,
Yunus
 

 

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[Freesurfer] Help

[Xincen Wu]

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Hi,

I am using freesurfer. I have gone through with the installation and
diagnostics and everything works fine. FOr example, using the command
recon-all --help in terminal yields a bunch of directions. Yet, when I
enter something like: recon-all -s bert -autorecon1

an error pops up saying my python3 is problematic. However, I regularly use
python3 and redownloaded it after. Please advise on the issue at hand.

Thanks,
Lucas
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Re: [Freesurfer] freesurfer results QC

[Diers, Kersten /DZNE]

External Email - Use Caution

Hi Yununs,

thanks for your mail:

There are no fixed and hard thresholds for these metrics (e.g., SNR). It really 
depends on the sample and image characteristics. More important than the 
absolute values is the distribution of these values across cases; that is, we 
typically use them to check if are there any images that have very different 
values than the others (outliers). These images would then require closer 
inspection.

Best,

Kersten

On Sun, 2023-11-19 at 07:47 +, yunus soleymani wrote:

CAUTION: This email originated from outside of DZNE. Do not click links or open 
attachments unless you recognize the sender and know the content is safe.
ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim 
Anklicken von Links oder Öffnen von Anhängen


External Email - Use Caution

Hi Freesurfer users,

I have recently used the FSQC algorithm 
(https://secure-web.cisco.com/1mLeKlIR1q8rizh6y08qBZ7PKZdlD2oOwA4tnpgsO99TKEwYIOck4qrzXrqboQAna9vs7TzIREN33RyB-cbnZO-ttU5q7hQWt71nEF1O1tJq1AlaffzdqQJNQkwfBtfgHBKjR1-r3ChazkCzlhE-IM7p1a9vAz5jp4GxHERnsJxiSk0d5H-7MAAijSSbuXhkMazQgq1M6kVbKsGWu-5cFnAfwSiqayCc24aWMfL79YfHbExpTjPjfbWKMOLtgUQtdUHkmbatJVNIUT4SA59EHhp1rFY0s5ip0_F11XjnHmF5gmReH1q2S6AYjY5iJ8cyWx132SZsmDIa91qa0faYthA/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc%23usage)
 to check the quality of my Freesurfer volumetric results. However, I am having 
trouble understanding the meaning of the output numbers. What is the acceptable 
threshold number of SNR? I would appreciate any help you can provide.

Thank you,

Yunus








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