External Email - Use Caution
Many thanks for the answer! Sorry, there seems to be some context
missing. I was replying to an old post from the archives and thought it
would attach itself there. I copied the script for mri_glmfit-sim from
that post.
Here is the link to it:
https://secure-web.cisco.com/15BtKLUwfY0w8EfmB_-A7ZDaRheinuB5VHF9HK_Z18GRANEdswic5J7pcj25pj0DdPtIBdiTNihFw4d9O3kSZ2POcICTSbzx2tU55-3U8efdnnwSXSenRJdCAo9BeVRNoGbEkHMM4kss4LLfErQthEvM3LMag5cc8E660zxZ49G95xa3QAFbvVMQTHlL-FlOW3Fw0aExkHQpQat4pdP6rHFb4XTxc2eCnySWqcz5YtcBSRDFRGIl0hO-KNzOddOwJ8AkckzV3fkeLpetEtQx7E4XAgixFbbXCNk8FzjrTHjSYTrj3_OlZLCjcYst5mF1c/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68973.html
I think the mistake is that I didn't convert it into a script properly.
Could you perhaps provide me with the script as a file? I would like to
get the volume of each subject from the ocn.dat by adding --spatial-sum
to the command line. Exactly as described in the post.
Best
Sven
Am 06.02.24 um 15:16 schrieb Huang, Yujing:
I can’t reproduce the error here with FS 6.0. Not sure where you
downloaded the script. Can you run this “tcsh -x
$FREESURFER_HOME/bin/mri_glmfit-sim –help”? I’m hoping it will give
some hints.
Best,
Yujing
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Sven Kühn
*Sent:* Sunday, February 4, 2024 12:09 PM
*To:* Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu>;
freesurfer@nmr.mgh.harvard.edu
*Subject:* Re: [Freesurfer] Unit of the Numbers in
cache.th40.neg.y.ocn.dat
* External Email - Use Caution *
Hi Dr. Greve, hi all
I have tried your code. I copied it from the website into a text file
and replaced mri_glmfit-sim in the freesurfer/bin folder. The file is
executable but aborts after a few lines with no indication of a cause.
The following output is generated:
/xx@xxx:~/Schreibtisch/WMH_DCS$ mri_glmfit-sim --glmdir
rh.volume.DCS.10.glmdir --cache 2.3 abs --cwp 0.05 --2spaces --spatial-sum
cmdline mri_glmfit.bin --y rh.volume.DCS.10.mgh --fsgd
FSGD/DCSstudy.fsgd --C Contrasts/DCS-DCSK.mtx --C
Contrasts/DCSK-DCS.mtx --surf fsaverage rh --cortex --glmdir
rh.volume.DCS.10.glmdir
SURFACE: fsaverage rh
Unmatched `./
Even if I run --help, only some of the lines appear:
/mri_glmfit-sim --help
--glmdir glmdir
--cwp cwthresh : cluster-wise p-value threshold (.05)
Use pre-computed z-based monte-carlo simulations (see mri_mcsim)
--mczsim vwthreshold sign
If you have run your own simulations (mri_mcsim), then specify
--mczsim-dir dir : default is FREESURFER_HOME/average/mult-comp-cor
--mczsim-label label : default is cortex
Use permutation simulation
--perm nsim CFT sign : permutation simulation with nsim iterations
Unmatched "./
Do you have any idea why this might be?
Like Xiaoxu before me, I have already tried to convert the file with
dos2unix. However, without the desired effect.
I am using Linux Ubuntu 16.04 and Freesurfer Vers. 6.0.
I would be very grateful for any tips.
Best regards
sven
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://secure-web.cisco.com/1dOpF92NtrTpxumyDbAlH8IN1EBeFBZrxV_obr2KSDtkHnxRBVS1r6-fjccOS3_EGHAoSFxjO1Pvnguvm2CJ5yvyHIOenP8t-Zp9rz5FQR6gwArQmn_BvfumQwEbodi-K8XnTD5SrM4prLfkzI1eZBR-W9tQSpZ3NX_P3HKWrxbmeJZ9d7jlSrFNvVoKPbfJlVQmLChsnj-Ap2_LwI4L3Vu6_E-X898JUTPtCVJ-Y7cj71WR6OWa6d9V_-Hf0qkerJp7YAAZahSpw_1dmPzuQV_YIbZDI-5cceFqTzEV-GxUczkeAoPcPql3-BItuCLCq/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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://secure-web.cisco.com/1EYZzzWWmgh3TVmqWgTDozSTTXs8FNuPvTMSrbRc7cLIAGWR_mfoBX1FZX2Zoxru0z8d1195za8JcdynO5g7Fo1wxptjBxg2NLFSAn6pcJ-pnuru3VhMXJU98rA3Vd1SP1VP6Z7_14gtytrVa0B_vgG4VyRYS-BI8-EBeGMH8sDcvelrt0M_CK-6GMJQVvPTBftTqUIWAv9daYyNoZSXvcaiVIaLK-VVWORCMdTY7xozFECDJbQ4aoOVwzDcmQAwiQVc-NP4BEZXA77CJz0UJk4KpNZIWeP4_3azckePccY2oQ0VLL1G87uwIJMWyt7X-/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
<https://secure-web.cisco.com/1EYZzzWWmgh3TVmqWgTDozSTTXs8FNuPvTMSrbRc7cLIAGWR_mfoBX1FZX2Zoxru0z8d1195za8JcdynO5g7Fo1wxptjBxg2NLFSAn6pcJ-pnuru3VhMXJU98rA3Vd1SP1VP6Z7_14gtytrVa0B_vgG4VyRYS-BI8-EBeGMH8sDcvelrt0M_CK-6GMJQVvPTBftTqUIWAv9daYyNoZSXvcaiVIaLK-VVWORCMdTY7xozFECDJbQ4aoOVwzDcmQAwiQVc-NP4BEZXA77CJz0UJk4KpNZIWeP4_3azckePccY2oQ0VLL1G87uwIJMWyt7X-/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>
.
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 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
<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.
