Re: [Freesurfer] recon-all cannot execute: required file not found

[fsbuild]

External Email - Use Caution

I don’t see what FREESURFER _HOME is set to, but if you used the .deb package 
installer, it would be /usr/local/freesurfer/7.4.0, i.e.
$ wget 
https://secure-web.cisco.com/1vzo5wK6ItFFFMnllsCMKRTIzcqYXDSETeXibiyz78VEk_TVHkbVLtjlltPd0g0Uvd8x0WK89GE8gU1KWFMzKnfwwgiI7LxjmgavQJ6CRuDKNdbu69lRngmJXHI_jT7Apzbthify1jBVr0Rl4tHRLO59uiYFLhP5xVv4FxnW-1brLM5t_f80dYxYqxS-tDJmUcSQBJ26bUuIwdNXHT49QU9R4-QLIUjxabN7pBG7dNNvYjk6etULRIlRTmLlKSxZ11x1M0Be8QDGN-sL353J66YtQqcu9Ew-9KlI2nYNXikCfbW-0PZolvzHu35pUzJw_8zpHpyEpfdmLOKtTKWv0Iw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Fpub%2Fdist%2Ffreesurfer%2F7.4.0%2Ffreesurfer_ubuntu22-7.4.0_amd64.deb%24
 sudo apt-get install ./freesurfer_ubuntu22-7.4.0_amd64.deb… answer yes to all 
queries ….,.. output deleted ...
$ export FREESURFER_HOME=/usr/local/freesurfer/7.4.0$ source 
$FREESURFER_HOME/SetUpFreeSurfer.sh… output deleted …
$ which recon-all
/usr/local/freesurfer/7.4.0/bin/recon-all
$ recon-all -version
freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e
If you used the tar file instead, then some permissions might not be correct 
depending upon how/where it was unarchived (and some dependencies might be 
missing).
- R.

On Jan 19, 2024, at 15:20, Peled, Noam,PhD npe...@mgh.harvard.edu 
wrote:I'm just trying now to runthe "recon-all -version", also without 
any arguments.Both produce the same 
error.Thanks!NoamFrom:freesurfer-boun...@nmr.mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing 
yhuan...@mgh.harvard.eduSent:Friday, January 19, 2024 3:10 
PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] recon-all 
cannot execute: required file not foundI’m wondering how you ran 
recon-all. Do you see the error even running it w/o any 
arguments?From:freesurfer-boun...@nmr..mgh.harvard.edu 
freesurfer-boun...@nmr.mgh.harvard.eduOn Behalf OfPeled, 
Noam,PhDSent:Friday, January 19, 2024 2:59 PMTo:Freesurfer support 
list freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] 
recon-all cannot execute: required file not foundThanksYujing,Yes, 
I looked for the file permissions using ls -l. It does have execute 
permissions.I also tried running chmod which didn't 
help..Thanks,NoamFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.edu
 on behalf of Huang, Yujing yhuan...@mgh.harvard.eduSent:Friday, 
January 19, 2024 2:54 PMTo:Freesurfer support list 
freesurfer@nmr.mgh.harvard.eduSubject:Re: [Freesurfer] recon-all 
cannot execute: required file not foundAfter sourcing Freesurfer, 
$FREESURFER_HOME is added to the front of your $PATH.1. ‘ls -l 
$FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the execute 
permissions?2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the 
permissionBest,YujingFrom:freesurfer-boun...@nmr.mgh.harvard.edufreesurfer-boun...@nmr.mgh.harvard.eduOn
 Behalf OfPeled, Noam,PhDSent:Friday, January 19, 2024 2:42 
PMTo:freesur...@nmr.mgh.harvard.eduSubject:[Freesurfer] recon-all 
cannot execute: required file not foundDear group,I'm trying to run 
Freesurfer on digitalOcean server running Ubuntu 22.10(GNU/Linux 
5.19.0-46-generic x86_64)I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)After sourcing 
Freesurfer, recon-all gives following error:.../freesurfer/bin/recon-all: 
cannot execute: required file not foundOther functions, e.g. freeview, 
mri_info, all seem to work as expectedWould love some 
help.Thanks,Noam___Freesurfer
 mailing 
listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

___
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Re: [Freesurfer] FW: Create a Binarized ROI for Surface

[Na, Xiaoxu]

External Email - Use Caution

Hi Dr. Doug,

Thanks for your prompt reply!

I’m sorry it was not clear. Basically, I would like to extract the cortical 
volume for each subject using a pre-defined ROI. As I have already created the 
surface ROI, thanks to your answer on the official website, I have no further 
question now on ROI.

This group analysis can’s further survive the multiple correction using the 
mri_glmfit-sim that you gave me years ago, so there is no file like 
cache.th40.neg.sig.ocn.annot as before.

Instead, I tried to create a ROI and run command line as $mri_segstats --seg 
mask1.sm1.bin.mgh --exlude 0 --i groupAnalysis/lh.volume.g2v2.10.mgh --avgwf 
lh.volume.mask1.dat, where mask1.sm1.bin.mgh is the ROI and 
groupAnalysis/lh.volume.g2v2.10.mgh is the mris_proc processed file from a 
group of subjects. It did extract something, 1 number for each subject, but I 
believe there is a ratio or scalar between the actual volume of that vertex and 
those show in lh.volume.g2v2.10.mgh. Is there anywhere I can figure out where 
this ratio/scalar is? Thank you so much!


Regards,
Xiaoxu


From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Douglas N. Greve
Sent: Friday, January 19, 2024 3:16 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: Create a Binarized ROI for Surface

On 1/19/2024 3: 45 PM, Na, Xiaoxu wrote: External Email - Use Caution Dear 
Freesurfer Expert, While the sphere can only be drawn using that Dr. Doug 
suggested, the sphere option would mess up. Do you need help with this? If so, 
can you give
ZjQcmQRYFpfptBannerStart
This Message Is From an External Sender
This message came from outside your organization.
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On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:

External Email - Use Caution
Dear Freesurfer Expert,

While the sphere can only be drawn using that Dr. Doug  suggested, the sphere 
option would mess up.
Do you need help with this? If so, can you give more info?


I have a further question as using this ROI to extract surface information from 
?h.area and ?h.volume. I’m using the command line as below:
$mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i 
groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat

However, due to the calculation of surface and volume, we need another input of 
sum file (ASCII file), how can I do that before I can run the above?
Sorry, I don't know what you mean


Another simple question is, what is lh.volume.mgh in the group analysis folder 
processed by mris_proc? Is that a simple merge of all subjects lh.volume file? 
Why the number is between 0-10, is there any way I can put ?h.volume or ?h.area 
back to gain each subject’s real volume or area value on that surface vertex? 
Thank you so much!
This is a vertex-wise measure of volume of the cortex at that point. Eg, a 
given vertex has an area defined by the mean area of the triangles that abut 
it. When this  is multiplied by the thickness, you get a volume measure (we 
actually compute it differently using a truncated pyramid, but that's the basic 
idea). You can use this in a VBM-like analysis.



Regards,
Xiaoxu




From: Na, Xiaoxu
Sent: Wednesday, December 13, 2023 4:25 PM
To: Freesurfer support list 

Subject: Create a Binarized ROI for Surface

Dear Freesurfer Expert,

We would like to extract mean Cth values for each subject within a own-creaded 
ROI (surface defined), using freeview (for instance). Is it possible to create 
a ROI (i.e. spherical surface) surrounding a particular vertex of an sig.mgh 
file? (and then extract its mean Cth values for each subject)?

I think this is not a new question, and it was posted somehow on MailScanner 
has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
be 

Re: [Freesurfer] FW: Create a Binarized ROI for Surface

[Douglas N. Greve]

On 1/19/2024 3:45 PM, Na, Xiaoxu wrote:


External Email - Use Caution

Dear Freesurfer Expert,

While the sphere can only be drawn using that Dr. Doug  suggested, the 
sphere option would mess up.



Do you need help with this? If so, can you give more info?


I have a further question as using this ROI to extract surface 
information from ?h.area and ?h.volume. I’m using the command line as 
below:


$mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i 
groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat


However, due to the calculation of surface and volume, we need another 
input of sum file (ASCII file), how can I do that before I can run the 
above?



Sorry, I don't know what you mean


Another simple question is, what is lh.volume.mgh in the group 
analysis folder processed by mris_proc? Is that a simple merge of all 
subjects lh.volume file? Why the number is between 0-10, is there any 
way I can put ?h.volume or ?h.area back to gain each subject’s real 
volume or area value on that surface vertex? Thank you so much!


This is a vertex-wise measure of volume of the cortex at that point. Eg, 
a given vertex has an area defined by the mean area of the triangles 
that abut it. When this  is multiplied by the thickness, you get a 
volume measure (we actually compute it differently using a truncated 
pyramid, but that's the basic idea). You can use this in a VBM-like 
analysis.


Regards,

Xiaoxu

*From:* Na, Xiaoxu
*Sent:* Wednesday, December 13, 2023 4:25 PM
*To:* Freesurfer support list 
*Subject:* Create a Binarized ROI for Surface

Dear Freesurfer Expert,

We would like to extract mean Cth values for each subject within a 
own-creaded ROI (surface defined), using freeview (for instance). Is 
it possible to create a ROI (i.e. spherical surface) surrounding a 
particular vertex of an sig.mgh file? (and then extract its mean Cth 
values for each subject)?


I think this is not a new question, and it was posted somehow on 
*MailScanner has detected a possible fraud attempt from 
"secure-web.cisco.com" claiming to be* 
https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/QuestionAnswers 
, 
and *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/msg67677.html 
, 
but I’m still encountering questions.


These commands did run, but together they didn’t create a binarized 
mask with 1 for the sphere around the coordinates, and 0 for the other 
voxels. Would you recommend what I should change? Thank you so much!


$mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness 
--pdf sphere --sphere-center -7.4 67.22 60.27 --radius 5 --o 
delta.sm00.mgh


$mris_fwhm \

--smooth-only \

--subject fsaverage \

--hemi lh \

--i delta.sm00.mgh \

--niters 10 \

--o delta.sm10.mgh

$mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh

Regards,

Xiaoxu


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Re: [Freesurfer] Issue with mri_glmfit-sim

[Douglas N. Greve]

mmm, still not sure. I'm assuming that you don't really have those 
backslashes ("\") in there. Can you try it with mcz instead of perm just 
to see if you can get it running. I would also try version 7.4.1; 
version 6.0 is from a long time ago and so hard to debug.


On 1/19/2024 3:03 PM, O'Neill, Alexandra Grace wrote:

Hi Doug,

Thanks so much for getting back to me. Below is our previous 
correspondence:


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


*Date: *Friday, January 12, 2024 at 4:19 PM
*To: *freesurfer@nmr.mgh.harvard.edu 
*Subject: *Re: [Freesurfer] Issue with mri_glmfit-sim

I think v6 might be broken when using -bg. Try removing that.

On 1/8/2024 11:19 AM, O'Neill, Alexandra Grace wrote:



Hello FS community,

To correct for multiple comparisons for the results of a
parametric modulation GLM analysis, I have run mri_glmfit-sim
using Freesurfer version 6.0 with the following command:

mri_glmfit-sim \ --debug --glmdir

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepSec/OSGM/osgm
\ --perm 1000 2.0 abs \ --cwp 0.05 \ --2spaces \ --bg 1

The code completes without errors, however none of the output
files mentioned in this tutorial


 are
created. Below are the contents of the mriglm-fit.log file in case
that is helpful.*

*



$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago

cmdline mri_glmfit.bin --y

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz
--wls

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz
--fsgd /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd --osgm
--glmdir

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM
--surf fsaverage rh --fwhm 6

sysname  Linux

hostname tempest.nmr.mgh.harvard.edu

machine  x86_64

user     ago5

FixVertexAreaFlag = 1

UseMaskWithSmoothing     1

fwhm     6.00

niters    26.00

OneSampleGroupMean 1

y
 
/autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz

logyflag 0

usedti  0

FSGD /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd

labelmask
 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/fsaverage/label/rh.cortex.label

maskinv 0

glmdir

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM

IllCondOK 0

ReScaleX 1

DoFFx 0

wFile

/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz

weightinv  1

weightsqrt 1

ResidualFWHM 12.847434

SearchSpace 74490.844410

anattype surface

Do you have any idea how to fix this problem? Thanks so much in
advance!

Alexandra



*Alexandra G. O'Neill**(she/her)*

/Clinical Research Coordinator/
Massachusetts General Hospital
Department of Psychiatry
Division of Neuropsychiatry and Neuromodulation
149 13th Street, Charlestown, MA 02129

T: (617) 726-8753 | E: agone...@mgh.harvard.edu



Thank you,
Alexandra

*From:* Greve, Douglas N.,Ph.D. 
*Sent:* Friday, January 19, 2024 2:44 PM
*To:* O'Neill, Alexandra Grace ; Freesurfer 
support list 

*Subject:* Re: [Freesurfer] Issue with mri_glmfit-sim
Sorry, I already forgot  what the problem was. Can you include our 
previous correspondence? Also, make sure to reply to the list. Thanks!


On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:

Hi Doug,

Thank you for getting back to me. Unfortunately, the issue is
persisting, and the command is still running but with no output
files. Is there anything else that could potentially be the
problem? I’m attaching the most recent log file (as a txt file)
from the command I ran. Please let me know if any other
information would be helpful!

Thank you so much,

Alexandra


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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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continue to communicate over unencrypted e-mail. 

[Freesurfer] FW: Create a Binarized ROI for Surface

[Na, Xiaoxu]

External Email - Use Caution

Dear Freesurfer Expert,

While the sphere can only be drawn using that Dr. Doug  suggested, the sphere 
option would mess up.

I have a further question as using this ROI to extract surface information from 
?h.area and ?h.volume. I'm using the command line as below:
$mri_segstats --seg mask1.sm1.bin.mgh --exlude 0 --i 
groupAnalysis/lh.volume.g2v2.10.mgh --sumwf lh.volume.mask1.dat

However, due to the calculation of surface and volume, we need another input of 
sum file (ASCII file), how can I do that before I can run the above?

Another simple question is, what is lh.volume.mgh in the group analysis folder 
processed by mris_proc? Is that a simple merge of all subjects lh.volume file? 
Why the number is between 0-10, is there any way I can put ?h.volume or ?h.area 
back to gain each subject's real volume or area value on that surface vertex? 
Thank you so much!


Regards,
Xiaoxu




From: Na, Xiaoxu
Sent: Wednesday, December 13, 2023 4:25 PM
To: Freesurfer support list 
Subject: Create a Binarized ROI for Surface

Dear Freesurfer Expert,

We would like to extract mean Cth values for each subject within a own-creaded 
ROI (surface defined), using freeview (for instance). Is it possible to create 
a ROI (i.e. spherical surface) surrounding a particular vertex of an sig.mgh 
file? (and then extract its mean Cth values for each subject)?

I think this is not a new question, and it was posted somehow on 
https://secure-web.cisco.com/1p4y33YGPMt3Xr5IlZXBnYyxigfeQuk70cz1lkfaic6sGmC8qA5lauVhI1rT6YyYkzZwV4Nc5The50lU99NUP0P08OuZXZlGcV2awRfjyD8dnCwV-ej_DoLtv2aEl5L6H_XsKSYPlV5UQTHQOPgZ0OlzfqPWrMDLf7vEJTFgE0oIXHWTkjRWe-r_xTSUd-TnsGIxbMkTt75znip6awWwYkSDWqYBayh-gKCuDQewg8jam5eacT7xjQeIMCJ6PfiYZ6aRVvxfG53AvXI1SpeazLlp_w0DaKDZ2Z6lqz6bpU1tQe5fI97ACIq3V9v7itFjzK-EsQ3hCBgBEt6pwsZjn4A/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsTutorial%2FQuestionAnswers,
 and 
https://secure-web.cisco.com/12Y_VHmZg0jaAJhDvwanhu4ZGApCQtSL5-3ja3GQFrxICAVdi67GO2_8gR_lTnHYtHR-MwxWWNBDNvMEJa9c08yx0yD-X9H7YpltRixy_yTVNWDoEFmPbXVe8Aa7ObaVpP8hW0jDh-1XV-er4q9cb7punqN6dsMDnKqfCIjHj4acnDo_OC1hh6lPWT28HI4p229FEOm4tcYuBTHxAEZW-dOnvHLX_ez_m1JE33dEKJuGeJRSYhOIU1gN1SmQ5XS9xghPSHM1hldLDnfMElawFLYe6DgFpAfanXHSTixWUwyOi6ftUWtajsQslG1nG0QPgjVhOw7Q4dXRBtPKi1kWDoQ/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg67677.html,
 but I'm still encountering questions.

These commands did run, but together they didn't create a binarized mask with 1 
for the sphere around the coordinates, and 0 for the other voxels. Would you 
recommend what I should change? Thank you so much!

$mri_volsynth --template $SUBJECTS_DIR/fsaverage/surf/lh.thickness --pdf sphere 
--sphere-center -7.4 67.22 60.27 --radius 5 --o delta.sm00.mgh
$mris_fwhm \
--smooth-only \
--subject fsaverage \
--hemi lh \
--i delta.sm00.mgh \
--niters 10 \
--o delta.sm10.mgh
$mri_binarize --i delta.sm10.mgh --min 10e-5 --o delta.sm10.bin.mgh


Regards,
Xiaoxu

--
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the sole use of the intended recipient(s) and may contain confidential and 
privileged information. Any unauthorized review, use, disclosure or 
distribution is prohibited. If you are not the intended recipient, please 
contact the sender by reply e-mail and destroy all copies of the original 
message.
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receiving this message means you understand and accept this risk and wish to 
continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

I'm just trying now to run the "recon-all -version", also without any arguments.
Both produce the same error.

Thanks!
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 19, 2024 3:10 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


I’m wondering how you ran recon-all.  Do you see the error even running it w/o 
any arguments?



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found



Thanks Yujing,

Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.

I also tried running chmod which didn't help.



Thanks,

Noam



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found



After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the 
execute permissions?

2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission





Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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Re: [Freesurfer] recon-all cannot execute: required file not found

[Huang, Yujing]

I'm wondering how you ran recon-all.  Do you see the error even running it w/o 
any arguments?

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:59 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found

Thanks Yujing,
Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.
I also tried running chmod which didn't help.

Thanks,
Noam

From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 on behalf of Huang, Yujing 
mailto:yhuan...@mgh.harvard.edu>>
Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the 
execute permissions?

2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission





Best,



Yujing



From: 
freesurfer-boun...@nmr.mgh.harvard.edu
 
mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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Re: [Freesurfer] Issue with mri_glmfit-sim

[O'Neill, Alexandra Grace]

Hi Doug,

Thanks so much for getting back to me. Below is our previous correspondence:


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

Date: Friday, January 12, 2024 at 4:19 PM
To: freesurfer@nmr.mgh.harvard.edu 
Subject: Re: [Freesurfer] Issue with mri_glmfit-sim

I think v6 might be broken when using -bg. Try removing that.

On 1/8/2024 11:19 AM, O'Neill, Alexandra Grace wrote:



Hello FS community,



To correct for multiple comparisons for the results of a parametric modulation 
GLM analysis, I have run mri_glmfit-sim using Freesurfer version 6.0 with the 
following command:



mri_glmfit-sim \ --debug --glmdir 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepSec/OSGM/osgm
 \ --perm 1000 2.0 abs \ --cwp 0.05 \ --2spaces \ --bg 1



The code completes without errors, however none of the output files mentioned 
in this 
tutorial
 are created. Below are the contents of the mriglm-fit.log file in case that is 
helpful.




$Id: mri_glmfit.c,v 1.241.2.4 2016/12/08 22:02:40 zkaufman Exp $

cwd /autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago

cmdline mri_glmfit.bin --y 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz
 --wls 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz
 --fsgd /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd --osgm --glmdir 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM
 --surf fsaverage rh --fwhm 6

sysname  Linux

hostname tempest.nmr.mgh.harvard.edu

machine  x86_64

user ago5

FixVertexAreaFlag = 1

UseMaskWithSmoothing 1

fwhm 6.00

niters26.00

OneSampleGroupMean 1

y
/autofs/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/ces.nii.gz

logyflag 0

usedti  0

FSGD /cluster/eryilmaz/users/FSGD/18_NFE_Patients.fsgd

labelmask  
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/fsaverage/label/rh.cortex.label

maskinv 0

glmdir 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/OSGM

IllCondOK 0

ReScaleX 1

DoFFx 0

wFile 
/cluster/eryilmaz/users/NFE/NFE_Subjects_ago/Analyses_NFE/18_NFE_Patients/SIRPSEC_LOADREG_RH/LoadDepNorm/cesvar.nii.gz

weightinv  1

weightsqrt 1

ResidualFWHM 12.847434

SearchSpace 74490.844410

anattype surface







Do you have any idea how to fix this problem? Thanks so much in advance!

Alexandra



Alexandra G. O'Neill (she/her)


Clinical Research Coordinator
Massachusetts General Hospital
Department of Psychiatry
Division of Neuropsychiatry and Neuromodulation
149 13th Street, Charlestown, MA 02129

T: (617) 726-8753 | E: agone...@mgh.harvard.edu

Thank you,
Alexandra

From: Greve, Douglas N.,Ph.D. 
Sent: Friday, January 19, 2024 2:44 PM
To: O'Neill, Alexandra Grace ; Freesurfer support 
list 
Subject: Re: [Freesurfer] Issue with mri_glmfit-sim

Sorry, I already forgot  what the problem was. Can you include our previous 
correspondence? Also, make sure to reply to the list. Thanks!

On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:

Hi Doug,



Thank you for getting back to me. Unfortunately, the issue is persisting, and 
the command is still running but with no output files. Is there anything else 
that could potentially be the problem? I’m attaching the most recent log file 
(as a txt file) from the command I ran. Please let me know if any other 
information would be helpful!



Thank you so much,

Alexandra





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Re: [Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

Thanks Yujing,
Yes, I looked for the file permissions using ls -l. It does have execute 
permissions.
I also tried running chmod which didn't help.

Thanks,
Noam

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 on behalf of Huang, Yujing 

Sent: Friday, January 19, 2024 2:54 PM
To: Freesurfer support list 
Subject: Re: [Freesurfer] recon-all cannot execute: required file not found


After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.



1. ‘ls -l $FREESURFER_HOME/bin/recon-all’ to check if your recon-all has the 
execute permissions?

2. use ‘chmod +x $FREESURFER_HOME/bin/recon-all’ to grant the permission





Best,



Yujing



From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found



Dear group,

I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)

I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)

After sourcing Freesurfer, recon-all gives following error:

.../freesurfer/bin/recon-all: cannot execute: required file not found



Other functions, e.g. freeview, mri_info, all seem to work as expected



Would love some help.

Thanks,

Noam




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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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. 

Re: [Freesurfer] recon-all cannot execute: required file not found

[Huang, Yujing]

After sourcing Freesurfer, $FREESURFER_HOME is added to the front of your $PATH.

1. 'ls -l $FREESURFER_HOME/bin/recon-all' to check if your recon-all has the 
execute permissions?
2. use 'chmod +x $FREESURFER_HOME/bin/recon-all' to grant the permission


Best,

Yujing

From: freesurfer-boun...@nmr.mgh.harvard.edu 
 On Behalf Of Peled, Noam,PhD
Sent: Friday, January 19, 2024 2:42 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all cannot execute: required file not found

Dear group,
I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)
I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)
After sourcing Freesurfer, recon-all gives following error:
.../freesurfer/bin/recon-all: cannot execute: required file not found

Other functions, e.g. freeview, mri_info, all seem to work as expected

Would love some help.
Thanks,
Noam


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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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continue to communicate over unencrypted e-mail. 

Re: [Freesurfer] Issue with mri_glmfit-sim

[Douglas N. Greve]

Sorry, I already forgot  what the problem was. Can you include our 
previous correspondence? Also, make sure to reply to the list. Thanks!


On 1/19/2024 10:07 AM, O'Neill, Alexandra Grace wrote:


Hi Doug,

Thank you for getting back to me. Unfortunately, the issue is 
persisting, and the command is still running but with no output files. 
Is there anything else that could potentially be the problem? I’m 
attaching the most recent log file (as a txt file) from the command I 
ran. Please let me know if any other information would be helpful!


Thank you so much,

Alexandra

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[Freesurfer] recon-all cannot execute: required file not found

[Peled, Noam,PhD]

Dear group,
I'm trying to run Freesurfer on digitalOcean server running Ubuntu 22.10 
(GNU/Linux 5.19.0-46-generic x86_64)
I Downloaded freesurfer 7.4.0 
(freesurfer-linux-ubuntu22_x86_64-7.4.0-20230510-e558e6e)
After sourcing Freesurfer, recon-all gives following error:
.../freesurfer/bin/recon-all: cannot execute: required file not found

Other functions, e.g. freeview, mri_info, all seem to work as expected

Would love some help.
Thanks,
Noam


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continue communication over unencrypted e-mail, please notify the sender of 
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Re: [Freesurfer] conversion of D-K atlas

[Fischl, Bruce R.,PHD]

Maybe you can give us more details about what you are trying to do? Generate an 
fMRI time-series that is the average response in each cortical parcel? And 
subcortical structure? The subcortical segmentation is not Talairach, although 
I'm not sure that is relevant. Generating the average time series should be 
pretty straightforward if that is what you want (although Doug will know the 
commands better than I do)

Cheers
Bruce

From: Arkhipova Anna, MUDr. 
Sent: Friday, January 19, 2024 10:08 AM
To: Fischl, Bruce R.,PHD ; 
Freesurfer@nmr.mgh.harvard.edu; fischl 
Cc: phlus...@upol.cz; Jasenská Monika, Ing. 
Subject: Re: conversion of D-K atlas


External Email - Use Caution
Hi Bruce,

thank you a lot for your kind reply.
Unfortunately, we've got further question, since we tried the following command:

recon-all -sd $PWD/surf -all -i ./Mprage.nii.gz -s $PWD -parallel -openmp 
$num_cores

and acquired a cortical-level parcellation according to the D-K atlas, but the 
subcortical parcellation was produced (we think) automatically according to the 
Talairach atlas (see attached).

Actually, we would like to get time-series in 82 brain regions as per D-K 
atlas, which should generate a vector of size 82x1 according to the methodology 
of Poudel et al. J Neural Eng. 2021.

However, as you wrote that D-K atlas is only cortical, would you think that it 
is possible at all (to get cortical + subcortial via D-K)?
Or have we proceeded wrongly?

We are sorry for repeatedly bothering you..
(We have tried to contact for the atlas both prof. Killiany and dr. Desikan, 
who sadly passed away, and also asked dr. Poudel himself, but he suggested a 
different atlas (we are not sure why) without subcortical regions.)

Thank you very much again!

Best regards,
Anna and lab team

From: Fischl, Bruce R.,PHD 
mailto:bfis...@mgh.harvard.edu>>
Sent: January 9, 2024 3:48:23 PM
To: Arkhipova Anna, MUDr.; 
Freesurfer@nmr.mgh.harvard.edu; fischl
Cc: phlus...@upol.cz
Subject: RE: conversion of D-K atlas

Upozornění: Tento e-mail přišel z externí e-mailové adresy. Dbejte zvýšené 
opatrnosti při otvírání příloh a odkazů v textu mailu, nezadávejte svoje 
přihlašovací údaje.

Hi Anna



Parcellation is more than just format conversion - you need to map it onto the 
details of an individual subject's anatomy. In addition, the DKT atlas is only 
cortical. If you want subcortical regions in addition you should run recon-all 
as it will produce both.



Cheers

Bruce



From: Arkhipova Anna, MUDr. 
mailto:anna.arkhip...@fnol.cz>>
Sent: Tuesday, January 9, 2024 6:14 AM
To: Freesurfer@nmr.mgh.harvard.edu; 
fischl mailto:fis...@nmr.mgh.harvard.edu>>
Cc: phlus...@upol.cz
Subject: conversion of D-K atlas



External Email - Use Caution

Dear prof. Fischl,

We would like to kindly ask a question, if there is a way to convert Fressurfer 
Atlas Desikan-Killiany (lh and 
rh.curvature.buckner40.filled.desikan_killiany.2010-03-25.gcs) to Nifti file 
for parcellation of our resting-state fMRI data.

Although we have tried script mri_convert, we obtained only cortical regions, 
but we need also subcortical regions. Would it be anyhow possible?

Thank you so much in advance.

Sincerely yours,
Anna Arkhipova, MD

fMRI laboratory
Department of Neurology, Faculty of Medicine and Dentistry
Palacky University and University hospital Olomouc
Czech Republic





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Re: [Freesurfer] Applying Wang Atlas to Group Analysis Results in FreeSurfer

[Douglas N. Greve]

what is the wang atlas? volume or surface?

On 1/19/2024 12:20 AM, Sujeevini Sujanthan wrote:


External Email - Use Caution

Hi,

I would like to apply the wang atlas over the group activation maps 
produced from Freesurfer analysis. I would appreciate any 
guidance/instructions you can offer for how I can do that.


Thank you for your time!

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[Freesurfer] EasyReg question

[Èlia Pedregosa]

External Email - Use Caution

Dear Juan Eugenio Iglesias,

We are a biomedical engineering company (BIOREM) in Barcelona, and we are 
collaborating in a research and innovation project with the University of 
Barcelona.

For this project we use EasyReg to do brain registrations. However, we have 
some problems with the necessary memory to run the program. In that sense, we 
ask you which computational requirements we need.

If it is possible, could you provide us this information?

Thanks,
best regards.


Èlia Pedregosa Sandoval

BIOREM_biomedical engineering

Madrazo 68, bxs.

08006 BARCELONA

Telf. 934 186 129

http://secure-web.cisco.com/1_MkzRbqyiH66KINd6uLPW_76jujv3qAzV1ApABqrJsjeA59YoIvZKioXbhze-3PmTBPY4zYVPRbmUtnZfHA9Mc0LYXYJZ1hMPubrETPpVJgGeU26LFcqgWIvY-jR9zva52qUPhUDa7aNp__mga_PvV3MVUYWI0sXD8vJY17dfmMUX2rVXXtG0GoIEixVY2aIMx_LWq4wM43Ni1a5Ox5h2UshZ-jXp8WLeOKjrV5yhn4SqJ4oYxK_-marNRgaos-ULpaBXS5XF4W5ln7IHxOQetyxzYbIVdsSODeToI3r49WZDMq-xmIPRHQwVI-kqvRJ/http%3A%2F%2Fwww.biorem.cat

[cid:f6917007-7636-4b37-be0a-010ab3bd281d][cid:c6b9a427-fbb1-4f20-986e-499840b7bfe5]


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