date:20201117

Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump)

2020-11-17 Thread falk.luesebr...@med.ovgu.de

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Dear Kristine,


I haven't had any issues processing high resolution data with version 6 or 7 
using either the -cm or -hires flag. However, I never used the -cw 256 flag as 
my FoV was never greater than 256.


Could you post the size of the created files? Especially orig.mgz with and 
without using the cw256 flag? Have you tried to not include the T2 volume? Just 
an educated guess, but maybe cropping of the FoV is done on the T1 only and, 
therefore, results in the error you are facing due to the additional contrasts.


Best,

Falk




Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Lee Subin Kristine 

Gesendet: Montag, 16. November 2020 18:56:55
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Re: [Freesurfer] recon-all for 0.85 isotropic images error (bump)


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-Bumping this question up because still could not find a solution 

-Any contributions or ideas would be greatly appreciated -



I am still having problems with running the high resolution recon-all (on v.6.0 
stable).

I have tried multiple flags (-hires, -cm, with and without cw256), but they all 
lead to the same error message, basically saying that the orig.mgz  FOV is more 
than 256 (even when I try to conform the image to 256).

(ERROR! FOV=272.000 > 256)/



When I try recon-all.v6.hires, the rawavg.mgz is not able to be created.



I have tried on both Ubuntu 14.04 and 16.04, but still get the same results.



Has anyone had any success in using the hires option of recon-all?

Any input would be appreciated.



Best Regards,

Kristine





Windows 10용 
메일에서
 보냄



보낸 사람: Lee Subin Kristine
보낸 날짜: Friday, October 30, 2020 9:40 PM
받는 사람: freesurfer@nmr.mgh.harvard.edu
제목: recon-all for 0.85 isotropic images error



Hello FreeSurfer Developers,



I'm trying to run recon-all (v.6) on T1- and T2-weighted images that have 
0.85mm^3 isotropic voxels



I have entered the command as below,

with the T2, T2pial, cm, cw256 flags.



recon-all -i $T1_DIR/"oT1_"$subj.nii -T2 $T2_DIR/"oT2_"$subj.nii -T2pial -cm 
-cw256 -subject $subj"_test" -all



However, I keep getting the error as follows.



ERROR! FOV=272.000 > 256

Include the flag -cw256 with recon-all!

Inspect orig.mgz to ensure the head is fully visible.

I'm guessing that conforming to the small voxel size results in a FOV that is 
out of limit?

However, when I check the orig.mgz file it looks fine.

(It has an image dimension of 320 x 320 x 320).

Even when I include the flag -cw256 as the error message says, I still get the 
same error message.

(Also, I cannot find any documentation about the -cw256flag on the help page).



I have pasted the full log below.



Thank you for your help.



Best regards,

Kristine



-

subin@ubuntu:/mnt/hgfs/subindata/MYELIN-QSM/SCRIPT$ ./run_fs_1

INFO: all volumes are conformed to the min voxel size

Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

INFO: SUBJECTS_DIR is /mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW

Actual FREESURFER_HOME /usr/local/freesurfer

Linux ubuntu 4.15.0-112-generic #113~16.04.1-Ubuntu SMP Fri Jul 10 04:37:08 UTC 
2020 x86_64 x86_64 x86_64 GNU/Linux

'/usr/local/freesurfer/bin/recon-all' -> 
'/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/scripts/recon-all.local-copy'

-cw256 option is now persistent (remove with -clean-cw256)

/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test



 mri_convert /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii 
/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz



mri_convert.bin /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii 
/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz

$Id: mri_convert.c,v 1.226 2016/02/26 16:15:24 mreuter Exp $

reading from /mnt/hgfs/subindata/MYELIN-QSM/BRL_T1/oT1_BRL_0004.nii...

TR=2400.00, TE=0.00, TI=0.00, flip angle=0.00

i_ras = (0.8, -0.00515189, -0.00357438)

j_ras = (0.00515192, 0.87, 0)

k_ras = (0.00357433, -1.83865e-05, 0.94)

writing to 
/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test/mri/orig/001.mgz...

#

#@# T2/FLAIR Input Fri Oct 30 05:19:16 PDT 2020

/mnt/hgfs/subindata/MYELIN-QSM/FSoutputs_NEW/BRL_0004_test



 mri_convert --no_scale 1 
/mnt/hgfs/subindata/MYELIN-QS

[Freesurfer] T1 and DTI nifti data stored after running recon-all and trac-all

2020-11-17 Thread Zeng, Qi

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Hi,

I run both recon-all and trac-all for each subject. Where are the original
T1 and DTI data stored in the output files?
Thank you so much!

Best,
Qi
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[Freesurfer] problem about PVC of PETSurfer {Disarmed}

2020-11-17 Thread qianqiansci

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Hello Freesurfer,
We know that the freesurfer7 has given a new module to separate hippocampal 
subfields in MRI image, but we encoumter problems in registering the PET image 
with MRI image. We find that the resolution radio of PET image is not enough, 
it made the SUVr of hippocampal subfield we get is not accurate. So we want to 
use the PVC function of PETSurfer. Whether the PETsurfer output the result of 
PET image after PVC ? so that we can use it directly to registering with MRI 
image. If it doesn't output the result, can we save it in some ways? Thank you 
for your guidance.


| |
qianqiansci
|
|
qianqian...@163.com
|
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Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

2020-11-17 Thread 李梦君

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I got the sum area and average area of the label, there is no significant 
difference between the mTBI group and health control, either.However, the label 
was significant different in the fsaverage between mTBI group and health 
control after multiple control. Did this correct?


-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-16 23:48:37 (星期一)
收件人: freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

The lh_areapial.avgwf.dat has a value for each subject. That value will be 
whatever the y.mgh is. If you want a different value, then create a new y.mgh 
file. Also, I forgot to tell you to include --sumwf so that the avgwf file has 
the sum and not the average.


On 11/14/2020 5:24 AM, 李梦君 wrote:


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  I am sorry for that my presentation was not that good, the lh_areapial.sum 
and 


lh_areapial.avgwf.dat file are uploaded, I get only one area value in the 
lh_areapial.sum file 


with the following command.


mri_segstats 
--i qdec/Areapial_15_L/y.mgh 
--slabel fsaverage lh lh.areapial.label 
--avgwf lh_areapial.avgwf.dat 
--accumulate 
--sum lh_areapial.sum 
--exclude 0


My question was that how can I get the value of the area and volume in the 
standard space for every TBI and health control subjects. 






-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-13 23:03:50 (星期五)
收件人:freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} {Disarmed}

sorry, I don't know what you are asking


On 11/12/2020 8:30 PM, 李梦君 wrote:


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Thanks! I get only one area value in the lh_areapial.sum file with this command:


mri_segstats 
--i qdec/Areapial_15_L/y.mgh 
--slabel fsaverage lh lh.areapial.label 
--avgwf lh_areapial.avgwf.dat 
--accumulate 
--sum lh_areapial.sum 
--exclude 0


(1)Should I extract the area and volume one by one with the following command 
for each subject:


mri_segstats 
--i qdec/Areapial_15_L/y.mgh 
--slabel fsaverage lh subjid/label/lh.areapial.label(this label file was mapped 
to every subject from the fsaverage) 
--avgwf lh_areapial.avgwf.dat 
--accumulate 
--sum lh_areapial.sum 
--exclude 0


-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-12 22:23:13 (星期四)
收件人:freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed}

No, the area will be under the "Mean" column. Sorry, I know it is confusing. 
Also, you will just want to use the 2nd row. You can eliminate the first row 
with --exclude 0



On 11/12/2020 5:39 AM, 李梦君 wrote:


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Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after 
the mri_segstats command



(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?


(2) When I extract the volumes, the lh_volume.sum displays the unit for the 
volume is Area_mm2（Blue color). Is this correct?




ColHeaders  Index SegId NVertices Area_mm2  StructName  Mean  StdDev
  MinMax   Range  
  1   0161058 81037.1   Seg   242940.32810.7312 
0. 3.8885 3.8885 
  2   1  2784 1182.3Seg00013760.6619 0.2525 
0.7136 1.8140 1.1005 


Following is the code for extracting volumes
mri_segstats 
--i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.volume.label (This was the label extracted from the 
fsaverage after multi-correction)
--avgwf lh_volume.avgwf.dat (output file)
--accumulate 
--sum lh_volume.sum (output file)






-原始邮件-
发件人:"Douglas N. Greve" 
发送时间:2020-11-11 23:58:20 (星期三)
收件人:freesurfer@nmr.mgh.harvard.edu
抄送:
主题: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for 
every subject {Disarmed} {Disarmed} {Disarmed}

Sorry, try this


mri_segstats 
--i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the 
fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate 
--sum lh_areapial.sum (output file)
On 11/5/2020 10:26 PM, 李梦君 wrote:


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I tried following codes according to the suggestions, the terminal reported an 
error: cannot do frame average without input volume

mri_segstats 
--seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the 
fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate 
--sum lh_areapial.sum (output file)






-原始邮件-
发件人:"Douglas N. G

[Freesurfer] qdec replacement

2020-11-17 Thread Pagliaccio, David (NYSPI)

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Hello
I was just wondering if there were any updates on a FSv7 replacement for QDEC 
for vertex-wise cortical thickness analyses? Or if there were any 
recommendations for analyses in other programs?
Thanks!
David



--
David Pagliaccio, Ph.D.
Assistant Professor of Clinical Neurobiology (in Psychiatry)
Columbia University Irving Medical Center

Assistant Research Scientist
Division of Child and Adolescent Psychiatry
New York State Psychiatric Institute
1051 Riverside Drive
New York, NY 10032
phone: 646-774-5556
Email: 
david.pagliac...@nyspi.columbia.edu
Pronouns: he/him

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Re: [Freesurfer] distance between two vertices in Freeview

2020-11-17 Thread Wang, Ruopeng

Hi Mona,

The 3D scale bar in freeview is not for measurement. It is simply a scale bar 
for the field of view. I don’t think you can use that to measure the distance 
between two points.

Best,
Ruopeng

On Nov 17, 2020, at 11:45 AM, Nasiriavanaki, Zahra 
mailto:znasiriavan...@mgh.harvard.edu>> wrote:

Dear Freesurfer experts

Hi

I was trying to measure the dimensions of a surface ROI in a flatten map on 
Freeview. I used the 3D scale bar to measure the longest diameter of the ROI.
My question is how the scale bar is calculating the distance between the two 
points? Is it the euclidean distance between the two vertices?
I calculated the euclidean distance in matlab between the two vertices (using 
their x and y coordinates) , and the number I get, is much higher than what I 
see in freeview. I wonder why this discrepancy is happening?

I appreciate if you could please let me know the answer to my question.

Thanks
MOna

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

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[Freesurfer] Postdoctoral Fellowship in Cognitive Neuroscience - Braga Lab @ Northwestern University {Disarmed}

2020-11-17 Thread Ania Holubecki

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We are seeking a postdoctoral fellow to join the Braga Lab (
https://secure-web.cisco.com/1HqJOdOxFbbEvFFuelHbM7FlG-fov0-xk1W0oKrv-pXwn-hq9RbHq5BYpiT8F3AxYMaiFJo1mLAtSQN0snXlWOKseCYn4NtWCI36wWgdwkbF4bePFxDZy4sGlWhLqbiWfD4Y7gARsoxcdDuUQNroDUjqvRtTMlCSEL1nykx1jv-zZgEBDVqnd9BB9iwMDaKjeWnG5FvrsBZTF7o5_7GigTeLcvMF0por8t45ImXbVjj-Eh6xVT7YiGjVHkQJ3-7XsoyIBE-YaZIhLQfkcDj9Otw/https%3A%2F%2Fbragalab.com)
in the Department of Neurology at the Northwestern
University Feinberg School of Medicine. Under the mentorship of Rodrigo M.
Braga, PhD, the lab uses and develops neuroimaging techniques to
characterize brain network organization and function at the level of
individuals. Research topics include the nature of brain regional
specialization for language, recollection and mental imagery, as well as
the mechanisms of cross-network interaction at high spatiotemporal
resolution.

Fellows will assist with ongoing research studies using methodologies
including functional magnetic resonance imaging (fMRI), intracranial
electroencephalography (iEEG) and brain stimulation. Fellows will have
opportunities to participate and lead in data collection and analysis,
mentorship of students and staff, presentations at national meetings, and
writing publications.

Requirements: Applicants must have a PhD (or equivalent doctoral degree) in
neuroscience or a related field, from an accredited institution. Fellows
must receive their degree by the start of training or have received their
degree no more than five years ago. Candidates must be a U.S. citizen or be
eligible to work in the United States (after obtaining an appropriate visa).

Desired skills: Strong candidates will have prior experience with
programming and neuroimaging (broadly defined), including data collection
and analysis, as well as conducting behavioral experiments.

Interested candidates should email a cover letter briefly describing their
research interests and qualifications, a curriculum vitae, as well as the
names and contact information for three references to Anna Holubecki at:
anna.holube...@northwestern.edu

Northwestern University is an Equal Opportunity, Affirmative Action
Employer of all protected classes, including veterans and individuals with
disabilities. Women, racial and ethnic minorities, individuals with
disabilities, and veterans are encouraged to apply. Hiring is contingent
upon eligibility to work in the United States.
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[Freesurfer] distance between two vertices in Freeview

2020-11-17 Thread Nasiriavanaki, Zahra

Dear Freesurfer experts

Hi

I was trying to measure the dimensions of a surface ROI in a flatten map on 
Freeview. I used the 3D scale bar to measure the longest diameter of the ROI.
My question is how the scale bar is calculating the distance between the two 
points? Is it the euclidean distance between the two vertices?
I calculated the euclidean distance in matlab between the two vertices (using 
their x and y coordinates) , and the number I get, is much higher than what I 
see in freeview. I wonder why this discrepancy is happening?

I appreciate if you could please let me know the answer to my question.

Thanks
MOna

Zahra (Mona) Nasiriavanaki, M.D.
Postdoctoral Research Fellow
Department of Psychiatry
Massachusetts General Hospital
149 13th Street, 149-2615
Charlestown, MA, USA, 02129

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[Freesurfer] smoothing on ?h.w-g.pct.mgh files

2020-11-17 Thread Enrico Collantoni

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Dear Freesurfer experts,
I computed the gray to white matter signal intensity ratio using the
pctsurfcon command and extracted the ?h.w-g.pct.mgh files. How can I
conduct a smoothing procedure on these surface files?

Thanks for your help,


-- 
Enrico Collantoni
MD, Ph.D., Psychiatrist
University of Padua
Neuroscience Department
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Re: [Freesurfer] Cortical thickness volume ROI to surface {Disarmed}

2020-11-17 Thread Alina Rojas

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Thank you for your response! Here the commands:


#register image to MNIspace
flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out 
mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat
#Create a registration from the ROI-anatomical volume to a freesurfer template 
subject
fslregister --s fsaverage --mov mydata_T1_MNI.nii.gz  --reg tmp.dat
#Map the ROI-mask to the fsaverage surface, to create an fsaverage-ROI surface 
overlay.
mri_vol2surf --mov ROI_MNI.nii.gz --reg tmp.dat --projdist-max 0 1 0.1 --interp 
nearest --hemi lh --out lh.fsaverage.ROI_MNI.mgh —noreshape

tkmeditfv fsaverage lh inflated -overlay lh.fsaverage.M1_L.mgh -fthresh 0.5

I tried with another threshold, and to change it while in Freeview and it’s 
either the whole surface with the overlay or none.

Thank you for your help!

Alina Rojas 




> Am 16.11.2020 um 17:04 schrieb Douglas N. Greve :
> 
> please send the command line
> 
> On 11/16/2020 7:20 AM, Alina Rojas wrote:
>> External Email - Use Caution
>> 
>> Hello Freesurfer experts,
>> 
>> I am attempting to register a ROI (.nii) to the surface of fsaverage to get 
>> the statistical output on the cortical thickness. I followed your 
>> instructions on MailScanner has detected a possible fraud attempt from 
>> "secure-web.cisco.com" claiming to 
>> behttps://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness 
>> 
>>  but after mri_vol2surf I get this message, I can’t visualize the ROI on the 
>> surface. I I’m using Freesurfer 7.0.1. How can I solve this? Thank you, 
>> Alina Rojas.
>> 
>> srcvol = M1_L.nii.gz
>> srcreg = tmp.dat
>> srcregold = 0
>> srcwarp unspecified
>> surf = white
>> hemi = lh
>> ProjDist = 0.5
>> reshape = 0
>> interp = nearest
>> float2int = round
>> GetProjMax = 1
>> INFO: float2int code = 0
>> INFO: using NIfTI-1 qform 
>> Done loading volume
>> INFO: This REGISTER_DAT transform is valid only for volumes between  COR 
>> types with c_(r,a,s) = 0.
>> Input reg is register.dat
>>  original matrix ---
>>  1.0   0.0   0.0   2.49380;
>>  0.0   0.0   1.0  -22.50500;
>>  0.0  -1.0   0.0  -9.53872;
>>  0.0   0.0   0.0   1.0;
>>  original matrix ---
>> Reading surface /fsaverage/surf/lh.white
>> Done reading source surface
>> Mapping Source Volume onto Source Subject Surface
>>  1 0 0 1
>> using old
>>  2 0.1 0 1
>> using old
>>  3 0.2 0 1
>> using old
>>  4 0.3 0 1
>> using old
>>  5 0.4 0 1
>> using old
>>  6 0.5 0 1
>> using old
>>  7 0.6 0 1
>> using old
>>  8 0.7 0 1
>> using old
>>  9 0.8 0 1
>> using old
>> 10 0.9 0 1
>> using old
>> Done mapping volume to surface
>> Number of source voxels hit = 75073
>> Writing to lh.fsaverage.M1_L.mgh
>> Dim: 163842 1 1
>> surfcolor: Subscript out of range.
>> 
>> 
>> 
>> 
>> 
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>>  
>> 
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>  
>

[Freesurfer] question about PVC of PETSurfer

2020-11-17 Thread 蒋袁芳

External Email - Use Caution


Hello Freesurfer,
We know that the freesurfer7 has given a new module to separate hippocampal 
subfields in MRI image, but we encoumter problems in registering the PET image 
with MRI image. We find that the resolution radio of PET image is not enough, 
it made the SUVr of hippocampal subfield we get is not accurate. So we want to 
use the PVC function of PETSurfer. Whether the PETsurfer output the result of 
PET image after PVC ? so that we can use it directly to registering with MRI 
image. If it doesn't output the result, can we save it in some ways? Thank you 
for your guidance.___
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[Freesurfer] Error in longitudinal pipeline {Disarmed}

2020-11-17 Thread vittal korann

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Hi FreeSurfer experts

Recently I started working on the longitudinal data.
I followed the pipeline described in the below link.
Also, I attached my longitudinal table along with freesurfer data.

https://secure-web.cisco.com/1DF2osKRIq2P6tkekGvGP9JanombamauC9_0TALJPJG645SLU2nh7tn-7_Pvy4mAGFDL5ZCQ-7nneT9KS0HnlAHQkEgTQRGCCCzHgio8sX7vjjyGppJTWboaKSDyw-Emb4-rh28oW0PrE-Nusp0E04Lyjc7RCd6ky3Vd_b-qJNnV5rFSwgXhtQsRoeFjFOi3Ojoyx73rZ1EHogep7OdoR4FyFfCRcDXPjh75W06R6mf8KznMRV8DPDWgpJQZax9oOublzxs_CR0a6IbFmW8-XvA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FLinearMixedEffectsModels

I got the error while executing the following commands:

CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1] zeros(3,5)];

F_lhstats = lme_mass_F(lhstats,CM);

And the Matlab threw an error shown below

>> CM.C = [zeros(3,5) [1 0 0 0 0 0 0;-1 0 0 1 0 0 0;0 0 0 -1 0 0 1]
> zeros(3,5)];
> >> F_lhstats = lme_mass_F(lhstats,CM);
> Error using lme_mass_F (line 50)
> The number of colums in the contrast matrix CM(1).C is different from the
> corresponding number of fixed effects in stats(1).Bhat


Any help would be appreciated!

With regards
Korann


long.qdec.table.dat.xlsx
Description: MS-Excel 2007 spreadsheet
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