date:20230112

Re: [Freesurfer] mri_label2vol error

2023-01-12 Thread Shao-Min (Sean) Hung

External Email - Use Caution

Sure.

Here's the command line:
 --
mri_label2vol --label
/Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/Retinolabels/TF.label --temp
/Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/004/fmc.nii.gz  --reg
/Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/register.dof6.lta --subject
$subj --o /Users/xxx/Documents/MRI/UNSTP/data/$subj/bold/Retinolabels/TS.nii
--

Here's the terminal output:
--

INFO: subject not needed, igorning.

Number of labels: 1

/Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/Retinolabels/TF.label

Annot File:  (null)

Template Volume:
/Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/004/fmc.nii.gz

Outut Volume:
/Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/Retinolabels/TS.nii

Registration File:
/Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/register.dof6.lta

Fill Threshold: 0

Label Vox Vol:  1

ProjType:   (null)

ProjTypeId: 0

ProjStart:  0

ProjStop:   0

ProjDelta:  0.1

Subject:  UNSTP041

Hemi: (null)

UseNewASeg2Vol:  0

DoLabelStatVol  0

LabelCodeOffset  0

setenv SUBJECTS_DIR /Applications/freesurfer/7.1.1/subjects

7.1.1

Template RAS-to-Vox: 

-0.28571  -0.0  -0.0   32.0;

-0.0  -0.0  -0.28571   32.0;

-0.0   0.25000  -0.0   17.0;

-0.0  -0.0  -0.0   1.0;

Template Voxel Volume: 49

nHits Thresh: 0

Loading registration from
/Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/register.dof6.lta

regio_read_register: loading lta

RegMat: 

 0.99970   0.02364   0.00603  -6.19680;

-0.00433  -0.07116   0.99746  -14.83764;

-0.02401   0.99718   0.07103  -9.81828;

 0.0   0.0   0.0   1.0;

Label RAS-to-Vox: 

-0.28563  -0.00676  -0.00172   33.77051;

 0.00686  -0.28491  -0.02029   34.80521;

-0.00108  -0.01779   0.24936   13.29059;

 0.0   0.0   0.0   1.0;

nlabels = 1

Allocating Hit Volume (139264) voxels

Loading
/Users/xxx/Documents/MRI/UNSTP/data/UNSTP041/bold/Retinolabels/TF.label

ERROR: label is not in tkreg coords so you need to specify atemplate with
--tkr-template MRI. The MRI should be the volumethat the label was created
on

--


There was something I forgot to mention. I also suspect that the problem
came from ROI creation. The ascii label column shows -1 for all
coordinates.


Thank you!

Sean

On Thu, Jan 12, 2023 at 11:29 PM Douglas N. Greve 
wrote:

> Can you send your command line and full terminal output?
>
> On 1/8/2023 9:37 PM, Shao-Min (Sean) Hung wrote:
>
> External Email - Use Caution
> Dear Doug,
>
> I have been having the following issue and haven't figured out a way to
> get around it. I have also searched the archive and did not find
> anything relevant enough to be helpful.
>
> The context is, I am drawing functional ROIs on volumetric data using
> FreeView. After which, I use mri_label2vol to convert the label into a
> volume for further analysis.
>
> I keep getting the following error:
>
> ERROR: label is not in tkreg coords so you need to specify atemplate with
> --tkr-template MRI. The MRI should be the volumethat the label was created
> on
>
> I used different templates to re-create the label but did not solve the
> issue. Using a different template for mri_label2vol did not seem to help
> either. I went back to check the labels, which seemed to be correctly drawn.
>
> Could you give me some directions to solve this issue? Thank you for your
> help!
>
> Regards,
> Sean
>
>
> ___
> Freesurfer mailing 
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
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>  <
>

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

2023-01-12 Thread Huang, Yujing

Hi Livia,

Yes, put /home/lirh717c/Desktop/V5LGN/ in front of .nii.gz in the command.

SUBJECTS_DIR is not used to find images specified in recon-all command line.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 12:06 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found


External Email - Use Caution
Dear Yujing,

Thank your for your fast reply. So you mean that I need to paste the whole path 
(home/../../..) before the name of the .nii.gz file in the command ?

It is weird, because I have always used it as sent and it worked until today. 
My subjects directory (called V5LGN, see mail below) contains all compressed 
nifti files of my subjects and additional output directories of the 
successfully processed subjects. This is why I thought that with the 
specification of SUBJECTS _DIR freesurfer knows where the subjects called are 
since they are there on this level without any subdirectories...?

Best
Livia

Von: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 im Auftrag von Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Gesendet: Donnerstag, 12. Januar 2023 17:53:41
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

Best,

Yujing

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be 
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



This applies not only to one file, but for all of them. I have also tried to 
rerun recon-all of another file that had been successful in december, I have 
also copied and renamed it to not overwrite it.. but none of the data sets were 
found!



For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the 
source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR

 freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME   /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lirh717c/Desktop/V5LGN
MNI_DIR   /freesurfer/mni



After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my 
files. Additionally, I can open freesurfer now and open

the scans within freeview, so that the following appears to me:

- my data are okay and I can open them

- freesurfer is generally running (only thing is one warning: (process:3965): 
Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.

Using the fallback 'C' locale.)

- even if setting subjects directory to another directory, it is not

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

2023-01-12 Thread Livia Ruehr

External Email - Use Caution

Dear Yujing,

Thank your for your fast reply. So you mean that I need to paste the whole path 
(home/../../..) before the name of the .nii.gz file in the command ?

It is weird, because I have always used it as sent and it worked until today. 
My subjects directory (called V5LGN, see mail below) contains all compressed 
nifti files of my subjects and additional output directories of the 
successfully processed subjects. This is why I thought that with the 
specification of SUBJECTS _DIR freesurfer knows where the subjects called are 
since they are there on this level without any subdirectories...?

Best
Livia

Von: freesurfer-boun...@nmr.mgh.harvard.edu 
 im Auftrag von Huang, Yujing 

Gesendet: Donnerstag, 12. Januar 2023 17:53:41
An: Freesurfer support list
Betreff: Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/188SCSXJL6xo2VGEo8HgYHx-r8WYg6qIHHBrJ5H8jADmFD7EkFuJdKFoqlV-t-VuYAfJbSFMnLOrvu_BlGnmpk4fgygDqyDiV64_LMs61QU9jtUqb0B-Uqqoe5kMGs7yZDpO1ga8B5uXjs_T5a5SzUNvszvbEXgdSW53Pn6gW4T02RH4C5SUwaUhhZ0JZuFdJdvOuf7iSsdGNzXNpjNVoVL5fgwVDUzSAuyTypmUncNw7WmScPwsSuHAfjOw4V_GRigrasjDayhnpCVqPiuf6ip6Exro1m5L9PVxaiNL6tcdHHEHcwHyFlgGzahojKSo2HNFTQuGSWiFcieUr-Wlb-Q/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting



This applies not only to one file, but for all of them. I have also tried to 
rerun recon-all of another file that had been successful in december, I have 
also copied and renamed it to not overwrite it.. but none of the data sets were 
found!



For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the 
source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR

 freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME   /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lirh717c/Desktop/V5LGN
MNI_DIR   /freesurfer/mni



After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my 
files. Additionally, I can open freesurfer now and open

the scans within freeview, so that the following appears to me:

- my data are okay and I can open them

- freesurfer is generally running (only thing is one warning: (process:3965): 
Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.

Using the fallback 'C' locale.)

- even if setting subjects directory to another directory, it is not working, 
the problem is neither the data nor the directory

- the subjects directory has correctly been set and I can access it --> my 
files are seen here

To this reason, I have no ideas anymore.

I am looking forward to your reply!



Kind regards

Livia Rühr

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

2023-01-12 Thread Huang, Yujing

Hi Livia,

SUBJECTS_DIR is the root directory for recon-all processed data. Each 
individual subject will have a separate subdirectory under SUBJECTS_DIR.

You need to specify full path to your images in recon-all command line.

Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Livia Ruehr
Sent: Thursday, January 12, 2023 11:31 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] WG: Problem with recon-all --> nii.gz file not found


External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,



for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".



I am using the following layout:
recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting



This applies not only to one file, but for all of them. I have also tried to 
rerun recon-all of another file that had been successful in december, I have 
also copied and renamed it to not overwrite it.. but none of the data sets were 
found!



For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the 
source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR

 freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME   /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lirh717c/Desktop/V5LGN
MNI_DIR   /freesurfer/mni



After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my 
files. Additionally, I can open freesurfer now and open

the scans within freeview, so that the following appears to me:

- my data are okay and I can open them

- freesurfer is generally running (only thing is one warning: (process:3965): 
Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.

Using the fallback 'C' locale.)

- even if setting subjects directory to another directory, it is not working, 
the problem is neither the data nor the directory

- the subjects directory has correctly been set and I can access it --> my 
files are seen here

To this reason, I have no ideas anymore.

I am looking forward to your reply!



Kind regards

Livia Rühr

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail.

[Freesurfer] WG: Problem with recon-all --> nii.gz file not found

2023-01-12 Thread Livia Ruehr

External Email - Use Caution




Von: Rühr, Livia
Gesendet: Donnerstag, 12. Januar 2023 17:25
An: freesurfer@nmr.mgh.harvard.edu
Betreff: Problem with recon-all --> nii.gz file not found


Dear Sir or Madame,


for my thesis I am running recon-all on my subjects' nii.gz T1-weighted scans. 
I use Freesurfer 7.0 on a Linux Mint 21"Vanessa".


I am using the following layout:

recon-all -s sub-03 -i sub-03-ses-01_T1w.nii.gz -all
This worked for me in december, whereby all my subjects were processed 
successfully and freesurfer created the directories. However, today I wanted to 
continue my work, but now it says that the file "sub-03-ses-01_T1w.nii.gz" ist 
not found (error message):
ERROR: cannot find sub-03-ses-01_T1w.nii.gz
Linux bam7-mint-chel 5.15.0-47-generic #51-Ubuntu SMP Thu Aug 11 07:51:15 UTC 
2022 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-03 exited with ERRORS at Thu Jan 12 16:59:42 CET 2023

For more details, see the log file
To report a problem, see 
http://secure-web.cisco.com/1z5XiLDbECZb1gv8wAZoV7fS7G_v-k4oqEkA6DCAbe1thCcFIbS8GrQ0rS8w87N0NvMiViBC0YdMwaSaNISpucIX_cXOR8Hlw_ctEC62zngdG7q65p1DvP0YEfI9NnWKw3M1gYslcsl2tUv-Rh3BP6QxrO1ymv8XqcmTbQMCeUWdSmpHoqxpNSBXWaMEYy7Zw-bi64zh_PeVMokZOpHriW3PchKqGpcU17Ubb_PerNQC-SYxuU-kUQ9F4W3ZBf55XZHT1fIDZpu3-5LlWFR5Y_0U_yCJUhW1Rb0WBZTbevTwP5zB5jEA72GyH4WJIzFT0DQk0ZNw8naeHaqRV0BVCKA/http%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBugReporting


This applies not only to one file, but for all of them. I have also tried to 
rerun recon-all of another file that had been successful in december, I have 
also copied and renamed it to not overwrite it.. but none of the data sets were 
found!


For Setup, I have defined my $FREESURFER_HOME, my $SUBJECTS_DIR and also the 
source (SetUpFreeSurfer.sh).

After typing the following: source $FREESURFER_HOME/SetUpFreeSurfer.sh

... I can now clearly see, that I am in the correct SUBJECTS_DIR
 freesurfer-linux-ubuntu22_x86_64-7.3.2-20220804-6354275 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /freesurfer
FSFAST_HOME   /freesurfer/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /home/lirh717c/Desktop/V5LGN
MNI_DIR   /freesurfer/mni

After navigating to this directory (cd $SUBJECTS_DIR) I can also see all my 
files. Additionally, I can open freesurfer now and open
the scans within freeview, so that the following appears to me:
- my data are okay and I can open them
- freesurfer is generally running (only thing is one warning: (process:3965): 
Gtk-WARNING **: 17:07:37.677: Locale not supported by C library.
Using the fallback 'C' locale.)
- even if setting subjects directory to another directory, it is not working, 
the problem is neither the data nor the directory
- the subjects directory has correctly been set and I can access it --> my 
files are seen here

To this reason, I have no ideas anymore.
I am looking forward to your reply!

Kind regards
Livia Rühr

___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is 
addressed.  If you believe this e-mail was sent to you in error and the e-mail 
contains patient information, please contact the Mass General Brigham 
Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline 
 .
Please note that this e-mail is not secure (encrypted).  If you do not wish to 
continue communication over unencrypted e-mail, please notify the sender of 
this message immediately.  Continuing to send or respond to e-mail after 
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Re: [Freesurfer] correlation analysis two groups (paired analysis)

2023-01-12 Thread Douglas N. Greve

If you are looking for the difference in the correlation between the 
groups then you have to use DODS and 0 0 1 -1. The way to understand it 
is that you have four regression coefficients and each means something. 
The way you have it set up in the fsgd file is that they are

1. group 1 intercept
2. group 2 intercept
3. group 1 cognition slope
4. group 2 coginition slope
Each coefficient gets multipled by its corresponding weight in the 
contrast and then the results are summed. So if you use 0 0 1 -1 you end 
up with contrast = g1cogslope-g2cogslope which is the difference you want


If you are just interested in whether the cog slope changes without 
regard to the group, then you would use 0 0 0.5 0.5 which means contrast 
= 0.5*g1cogslope + 0.5*g2cogslope which is the average of the slopes. In 
this case, using DOSS and 0 0 1 will give you the same results if there 
is no difference in the cog slopes between the groups




On 1/12/2023 8:48 AM, Agurne Sampedro Calvete wrote:


External Email - Use Caution

Dear FreeSurfer experts,

I have two groups and two time points and I would like to do a 
correlation analysis between a variable (cognition) and the change 
score in cortical thickness between the two time points (time2 minus 
time1).


I would like to see if the *correlation *is *different *among each 
group, if there is an interaction with the group.


I have followed the paired t test instructions (*MailScanner has 
detected a possible fraud attempt from "secure-web.cisco.com" claiming 
to be* https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis 
), 
but I am not sure about the contrast(s) I have to use.


The paired-diff.fsgd file (second fsgd file) is the following:

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables cognition
Input subject1pair Group1 0.546
Input subject1pair Group2 -0.243
...

How should it be the contrasts files to see the *correlation *of the 
variable cognition with the change score in thickness taking into 
account the groups? And should I use DODS or DOSS?


Using DODS:
0 0 0.5 0.5
 or
0 0 1 -1

I don't understand the difference between both contrasts. I think I 
should use the one of "0 0 1 -1" to see whether the cognition variable 
correlates with change in thickness differently according to the 
group. Is this correct?


Using DOSS:
0 0 1

Thank you very much in advance.

Kind regards,

Agurne






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Re: [Freesurfer] Do you have a specific reason for having only 3 motion regressors for connectivity analysis?

2023-01-12 Thread Douglas N. Greve

Not really. I think that 3 mostly spanned the space but I did not do any 
systematic tests. In general, I think you should be careful when adding 
regressors so 3 is more conservative than 6.


On 1/12/2023 4:40 AM, Andy Kim wrote:


External Email - Use Caution

Dear FreeSurfer Developers,

I am trying to analyze functional connectivity using Freesurfer. When 
I checked FSFAST tutorial, it says:
Sample command: "mkanalysis-sess -analysis fsrest.surf.lh -surface 
self lh -fwhm 5 -notask -nuisreg vcsf.dat 1 -nuisreg wm.dat 1 
-mcextreg -polyfit 5 -nskip 4 -fsd fsrest -TR 4.5 -per-run"
-mcextreg means that only top 3 components (I checked it was first 3 
columns of mcprextreg) are used out of total 6 components. And indeed 
there are only 3 motion regressors in X.mat file.
Freesurfer uses AFNI program to get motion correction parameters and 
AFNI uses all 6 components. (*MailScanner has detected a possible 
fraud attempt from "secure-web.cisco.com" claiming to be* 
https://afni.nimh.nih.gov/pub/dist/edu/latest/afni_handouts/afni05_regression.pdf 
)

Do you have any reasons for having 3 as default?

Kind Regards,
Andy Junghyun Kim

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Re: [Freesurfer] FS FAST

2023-01-12 Thread Douglas N. Greve

Just the basic is ok. Although I have not done it in a while, you should 
also be able to use octave (which is free). Once you get octave install 
and in your path, set the env variable FS_USE_OCTAVE to 1. Like I said, 
I have not used it in a while, but it I think it should still work.


On 1/11/2023 9:31 AM, Justin Oh wrote:


External Email - Use Caution

Dear Freesurfer team,

I am new to freesurfer and I'm working on learning how to pre process 
and analyze resting state fMRI. It's my understanding that MATLAB and 
FSL have to run in the background from what I took away from online 
tutorials. Is there a specific program within MATLAB that is necessary 
or will purchasing the basic student package from MATLAB be sufficient?


Thank you for your time!
-Justin Oh

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Re: [Freesurfer] mri_mask error exits returns a zero exit status

2023-01-12 Thread Douglas N. Greve


yes, you are correct. I just fixed that, so it will be in the next release.

On 1/10/2023 4:14 PM, Aaron Tanenbaum wrote:


External Email - Use Caution

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

On Tue, Jan 10, 2023 at 12:23 PM Aaron Tanenbaum 
 wrote:


Hello,
FYI, I recently noticed that mri_mask returns a zero exit status
when it is unable to write the output.


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Re: [Freesurfer] Image filter

2023-01-12 Thread Douglas N. Greve


FS does not filter prior to segmentation

On 1/10/2023 12:35 PM, Ruifeng Dong wrote:


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Dear Freesurfer community,

I wonder if Freesurfer uses any filter to deal with the noise in the 
image, before segmentation. If so, is the filter spatially local or 
nonlocal?


Thanks.

Best,
Ruifeng

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Re: [Freesurfer] mri_label2vol error

2023-01-12 Thread Douglas N. Greve


Can you send your command line and full terminal output?

On 1/8/2023 9:37 PM, Shao-Min (Sean) Hung wrote:


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Dear Doug,

I have been having the following issue and haven't figured out a way 
to get around it. I have also searched the archive and did not find 
anything relevant enough to be helpful.


The context is, I am drawing functional ROIs on volumetric data using 
FreeView. After which, I use mri_label2vol to convert the label into a 
volume for further analysis.


I keep getting the following error:

ERROR: label is not in tkreg coords so you need to specify atemplate 
with --tkr-template MRI. The MRI should be the volumethat the label 
was created on


I used different templates to re-create the label but did not solve 
the issue. Using a different template for mri_label2vol did not seem 
to help either. I went back to check the labels, which seemed to be 
correctly drawn.


Could you give me some directions to solve this issue? Thank you for 
your help!


Regards,
Sean


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Re: [Freesurfer] freeview: set file as read only (@Ruopeng)

2023-01-12 Thread Douglas N. Greve


Not that I know of. Ruopeng would know for sure.



On 1/7/2023 5:00 PM, Aaron Tanenbaum wrote:


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Hello,
Is there a way to set a loaded volume as read only in freeview on the 
command line?


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[Freesurfer] correlation analysis two groups (paired analysis)

2023-01-12 Thread Agurne Sampedro Calvete

External Email - Use Caution

Dear FreeSurfer experts,

I have two groups and two time points and I would like to do a correlation
analysis between a variable (cognition) and the change score in cortical
thickness between the two time points (time2 minus time1).

I would like to see if the *correlation *is *different *among each group,
if there is an interaction with the group.

I have followed the paired t test instructions (
https://secure-web.cisco.com/11YHUupGYyGBe5w6QAQb3OOLcNluK0Tqv4VUmAmDx5wuogvWlaypoD3OpvEWBM2c4Wa29T38k5k4_bq_JXA-kc8P0mACbCulAMmVSDKvC4Tl7x6Gk2A_azFExScL0y5HFngabH5bZRoIDy_dKvAtXkXegvTr-2ftNMkD3TQlTwaQtCSI-0554BriqrUu1MKXy2ZDf8l6cSP5im59p93FqJma0yYa3cYXujDp-aXCIOKlUXzojlgBIskwrWMiPG0pmIn08tOj1OYgSExrdJrOrWu2iAIGdhvSK3iuWEQ7BCEp4De-DPfIldNoZfbygVQ1mrt9CvPacDWwenDkjC7Q40A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPairedAnalysis),
but I am not
sure about the contrast(s) I have to use.

The paired-diff.fsgd file (second fsgd file) is the following:

GroupDescriptorFile 1
Title OSGM
Class Group1
Class Group2
Variables cognition
Input subject1pair Group1 0.546
Input subject1pair Group2 -0.243
...

How should it be the contrasts files to see the *correlation *of the
variable cognition with the change score in thickness taking into account
the groups? And should I use DODS or DOSS?

Using DODS:
0 0 0.5 0.5
or
0 0 1 -1

I don't understand the difference between both contrasts. I think I should
use the one of "0 0 1 -1" to see whether the cognition variable correlates
with change in thickness differently according to the group. Is this
correct?

Using DOSS:
0 0 1

Thank you very much in advance.

Kind regards,

Agurne
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[Freesurfer] Do you have a specific reason for having only 3 motion regressors for connectivity analysis?

2023-01-12 Thread Andy Kim

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Dear FreeSurfer Developers,

I am trying to analyze functional connectivity using Freesurfer. When I checked 
FSFAST tutorial, it says:
Sample command: "mkanalysis-sess -analysis fsrest.surf.lh -surface self lh 
-fwhm 5 -notask -nuisreg vcsf.dat 1 -nuisreg wm.dat 1 -mcextreg -polyfit 5 
-nskip 4 -fsd fsrest -TR 4.5 -per-run"
-mcextreg means that only top 3 components (I checked it was first 3 columns of 
mcprextreg) are used out of total 6 components. And indeed there are only 3 
motion regressors in X.mat file.
Freesurfer uses AFNI program to get motion correction parameters and AFNI uses 
all 6 components. 
(https://secure-web.cisco.com/12TJnsSiUh4nUlS0evLlfL-8nA36tqM4rfztjSsg7-3om9_ecCtXvMBvPYqjf0sKuLiZQn8Kc4JVAk2siFc7R9b_03WI4ju9aoZaa3RGNddJ6rWZ77949c6bJObCxos0x--p6-WKy89GVF6NEuQO9XARbvrlbU6PLWE6fc8EKApLIwE4AGMBKvY8GTpm-48nuYCz_feKDKtqo16zRuvxsXg6N2ct9tZ20yPtnCKpIxjhGQCsa02IvnHKdk-8k7CQ1y_BIQqQHk0Qw8k9Rz7Ud2xDKE0T-4U98Ig-DPt_kvVbU8fAPplOTT4aQchdtENcKWfIFk8X9A8PX4HnK3pYsbg/https%3A%2F%2Fafni.nimh.nih.gov%2Fpub%2Fdist%2Fedu%2Flatest%2Fafni_handouts%2Fafni05_regression.pdf)
Do you have any reasons for having 3 as default?

Kind Regards,
Andy Junghyun Kim
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Re: [Freesurfer] mri_label2vol error

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

Re: [Freesurfer] Problem with recon-all --> nii.gz file not found

[Freesurfer] WG: Problem with recon-all --> nii.gz file not found

Re: [Freesurfer] correlation analysis two groups (paired analysis)

Re: [Freesurfer] Do you have a specific reason for having only 3 motion regressors for connectivity analysis?

Re: [Freesurfer] FS FAST

Re: [Freesurfer] mri_mask error exits returns a zero exit status

Re: [Freesurfer] Image filter

Re: [Freesurfer] mri_label2vol error

Re: [Freesurfer] freeview: set file as read only (@Ruopeng)

[Freesurfer] correlation analysis two groups (paired analysis)

[Freesurfer] Do you have a specific reason for having only 3 motion regressors for connectivity analysis?

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