[Freesurfer] fspalm: mri_surfcluster error: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white

2022-05-18 Thread Wenjun Huang 
External Email - Use Caution

I'm attempting to use fspalm (
https://secure-web.cisco.com/1zRz_KYc-Z02lCLizE3BUB2We3AfuiVlIxzRg5VijNOs5jbFNTJTdsU98fKu8B4Ug7TYv7ChunsJYQqBLlivaVExtNZMsiujGamhHbMgVd5e8gMBRoDT5FDcSuW2fWov5lk4ByGZ28rIRaQ2HnRlFnvMIEZWpxhLBplju5VXNTUE5gLBwoGTwTJj9fCbXxDadtapyfu50b8RAye6odptf1c7yn2K_LGrMaJ9tv3bJDj8P-w8vi4n7lI1Z_d0u2EqR5vhiAvppazpxbCNrT2H3h5DS90I6KPrBRsv3CtUmUcP5RcwsRYFWUuX4zf2N-EK6_-z1hnKUywQBQlL_S0WNjA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsPalm%3Fhighlight%3D%2528PALM%2529),
 and
I copied fspalm, mri_volcluster, and mri_surfcluster into
$FREESURFER_HOME/bin. But get error: MRISread(): could not open file
mri_surfcluster: could not read surface
/home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
Reading source surface
/home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
And after I copy mri_volcluster, and mri_surfcluster into
$FREESURFER_HOME/bin, I got this error when I run mri_glmfit-sim.
I wonder if it's because of my freesurfer's version? And if it works for me
if I get a newer version, will it be ok if I recon-all, mri_glm-stim,
mri_glmfit-sim on 6.0v and do the fspalm on 7.2v within one project?

I've searched the list and no similar errors have been reported. Does
anyone have any thoughts on how to trouble-shoot this one? Also, I've
attached the fspalm.log and in case it's of any use.

1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a

2) Platform: Ubuntu 18.04 LTS(Bionic Beaver)

3) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic
#113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64
x86_64 GNU/Linux

4) fspalm.log and perm.th40.abs.mri_glmfit-sim.log: see attached


fspalm.log
Description: Binary data


perm.th40.abs.mri_glmfit-sim.log
Description: Binary data
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Re: [Freesurfer] fspalm: mri_surfcluster error: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white

2022-05-18 Thread Wenjun Huang 
External Email - Use Caution

Many thanks!

Best,
Wenjun

On Thu, May 19, 2022 at 11:25 AM Wenjun Huang  wrote:

>
> I'm attempting to use fspalm (
> https://secure-web.cisco.com/1S6OBvGbwHzirkAMrYJCV1DnPYU6rqVdgNfbqZr3v4kh2AhisMH_o2B4ctKBGE4FkhmsZveqh7FVojVKVD3YjAmqiNG28mOnwaOVKpVLpx0VLOWhX1Iio4HgSMairdKAG_7esH0K4_aHxdxjS-R7FuNknof3fm0qqMTMZ6ZFoLu-K1qnDs7Uz1Dbf8JvEXQdzCDvTzjskiaONc2f3-srdyTM7E_ilcUOccNsAnwQ1CDLtdIPI5qtArn1w2cSVcjBmlt58kag2Vlv1GjN7SAYLskOC4IVk8bKMJUcsdO0AlcX3gV4PX7Ftr7L3_j3IPwizWjuMSpBWxNjA7Z94ks3UFA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsPalm%3Fhighlight%3D%2528PALM%2529),
> and I copied fspalm, mri_volcluster, and mri_surfcluster into
> $FREESURFER_HOME/bin. But get error: MRISread(): could not open file
> mri_surfcluster: could not read surface
> /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
> Reading source surface
> /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
> And after I copy mri_volcluster, and mri_surfcluster into
> $FREESURFER_HOME/bin, I got this error when I run mri_glmfit-sim.
> I wonder if it's because of my freesurfer's version? And if it works for
> me if I get a newer version, will it be ok if I recon-all, mri_glm-stim,
> mri_glmfit-sim on 6.0v and do the fspalm on 7.2v within one project?
>
> I've searched the list and no similar errors have been reported. Does
> anyone have any thoughts on how to trouble-shoot this one? Also, I've
> attached the fspalm.log and in case it's of any use.
>
> 1) FreeSurfer version: 
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>
> 2) Platform: Ubuntu 18.04 LTS(Bionic Beaver)
>
> 3) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic 
> #113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64 x86_64 
> GNU/Linux
>
> 4) fspalm.log and perm.th40.abs.mri_glmfit-sim.log: see attached
>
>
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[Freesurfer] questions about ThalamicNuclei.sh, segmentHA_T1.sh, segmentBS.sh

2022-05-18 Thread Wenjun Huang 
External Email - Use Caution

Hi,
I'm attempting to use segmentThalamicNuclei.sh(
https://secure-web.cisco.com/1RV2omTbdlZNcuz2LjtNOfF_gXU-a1Zh7ZafxTa7vX-y1Z1LZxS0Oc2hhSnAz_ddkvbDogx-Es0B0cIzDL7ZBQVIpT6ABl0fiNwLa2arhoBRKoZI3G7JqVRilClK3470W9etqhZAuTI73h8WIryqVSmuffGYEmzC_qBEEG32btzrOWzQMu9VOAIVKuqmj28MQsu5OXvYtyCs4cER6AMvnPgPPJI0vUS6YtpUl_HwDp7oWaSV9mRK8y-K_wP5aEbu9J7kJEPZWfWfOGAJMJGhb2lwlwY_UPazMa8IVL41TmNiDPm7g7M7rOhQaCy2au5RE7zQeKh_oFyOhOuSLImPFMQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FThalamicNuclei%3Fhighlight%3D%2528ThalamicNuclei%2529
),segmentHA_T1.sh(
https://secure-web.cisco.com/1LhDcP1FH1KgfwvDWIRfvii3lB4d3_LJAyFBfDkPRA2sC_0Hb8PNMeYhMI4NcKHMxlPmRPi6a9qXgRGWik2fB2-82jK9ni74aHwjLZvVGvpjm75zmea3jM8w6xCFA-ydJ6g4OvIlmk29qVbMc1syd4o90De5Epz4qQH5iiIsINRgNyCQuG4LkA4M6CrmRyTk6pnfdGsodL86IFMckJFrobbcG29giqQSvutjofQM_u0iSBE-9kdsYK1w08a61MhWqWKxVomOA9Xi15vAixROnyJNU6pD3aatFme0rJl-jqDDBUxIHdvvMw6ym-g6s04b_SgAnHVm0ya5BMT8lsIHSsg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FHippocampalSubfieldsAndNucleiOfAmygdala),
segmentBS.sh (
https://secure-web.cisco.com/1Zcp3K-vS0QBfdAhIw0PbtQM6onkntbEtV2RlFJ3B_lENy1E-wg27W_Gh0fGz82KSfAlOsZxX_v-7bWnUfdCo3RIiqi1IC4tko3xKJzlOn4RCQ54Y7FKBy_-sUsdyEEywe9DHLBxJ1pjnVFVVHt2fNK2Ekma3VtOJ24mwTYw9IYIINbggoa8yIEvZhFQR9pdz4gAh-8zxcFO5DCO0iIlezhB1tXTmtggLzgCmtVzepI4zoKCpyF9oEDq-Bx-w-YD5eJFfx2ZVrqjDyvdFNyI90b_OY9SVbeLcHwaFD5Tpyd8JlWxWb_Yzgpg9fs6a67VuZTpM2S06gsX3z9YVMm6CBA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures).
 But I
have done all the recon-all on version 6.0. So I wonder if it's ok if I run
recon-all on 6.0v and do the three segments on 7.2v within one project?

I've searched the list and no similar errors have been reported. Does
anyone have any thoughts on how to trouble-shoot this one?


Many thanks,
Wenjun

1) FreeSurfer version(recon-all):
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55

2) aFreeSurfer version(segmentThalamicNuclei.sh,segmentHA_T1.sh,segmentBS.sh):
freesurfer-linux-ubuntu18_x86_64-7.2.0-20210721-aa8f76b

3) Platform: Ubuntu 18.04 LTS(Bionic Beaver)

4) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic
#113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64
x86_64 GNU/Linux
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Re: [Freesurfer] fspalm: mri_surfcluster error: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white

2022-05-18 Thread Wenjun Huang 
External Email - Use Caution

And I also want to know how to change -annot within facepalm.
Many thanks


Wenjun

On Thu, May 19, 2022 at 11:26 AM Wenjun Huang  wrote:

> Many thanks!
>
> Best,
> Wenjun
>
> On Thu, May 19, 2022 at 11:25 AM Wenjun Huang  wrote:
>
>>
>> I'm attempting to use fspalm (
>> https://secure-web.cisco.com/1Kms3SLF3QITdqbnXhA6CeV_CN973GbftIJwlnELCCj_a47UXXrstWbosqVD6lw5Ea18vdBwooyFRu8w24AtYBTLH8U9FTOCD2z1rZ1yn8Cc3edbTw4of8TgVGDxOCNhKFO9fUNSwq4u6aQXjEy-3ldSSgUPZf3KHWcsvhGbaqvIoIPtjlKd-GuHtKkCDAxNC8jf3oGBtjb2Yy6Lho7EP-dl9ZjMnuLskz2BVHNLk91Z3hYFjWKVhFuU8AsMriDLrGIL4Q942pkirjSUJtQRvuV8Bc034DRsAcfxYQFfAL8x8rAI4zmeXZeu0jIPBshykvrHMKS9zPL7muBX8qKphJw/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsPalm%3Fhighlight%3D%2528PALM%2529),
>> and I copied fspalm, mri_volcluster, and mri_surfcluster into
>> $FREESURFER_HOME/bin. But get error: MRISread(): could not open file
>> mri_surfcluster: could not read surface
>> /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
>> Reading source surface
>> /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
>> And after I copy mri_volcluster, and mri_surfcluster into
>> $FREESURFER_HOME/bin, I got this error when I run mri_glmfit-sim.
>> I wonder if it's because of my freesurfer's version? And if it works for
>> me if I get a newer version, will it be ok if I recon-all, mri_glm-stim,
>> mri_glmfit-sim on 6.0v and do the fspalm on 7.2v within one project?
>>
>> I've searched the list and no similar errors have been reported. Does
>> anyone have any thoughts on how to trouble-shoot this one? Also, I've
>> attached the fspalm.log and in case it's of any use.
>>
>> 1) FreeSurfer version: 
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>>
>> 2) Platform: Ubuntu 18.04 LTS(Bionic Beaver)
>>
>> 3) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic 
>> #113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64 x86_64 
>> GNU/Linux
>>
>> 4) fspalm.log and perm.th40.abs.mri_glmfit-sim.log: see attached
>>
>>
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contains patient information, please contact the Mass General Brigham 
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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Re: [Freesurfer] fspalm: mri_surfcluster error: could not read surface /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white

2022-05-18 Thread Wenjun Huang 
External Email - Use Caution

Sorry for the typing error. How to change --annot within fspalm

Many thanks
Wenjun

On Thu, May 19, 2022 at 11:26 AM Wenjun Huang  wrote:

> Many thanks!
>
> Best,
> Wenjun
>
> On Thu, May 19, 2022 at 11:25 AM Wenjun Huang  wrote:
>
>>
>> I'm attempting to use fspalm (
>> https://secure-web.cisco.com/1P6HkzX875RFyYC5DsJmukY3Fbs-Qqtjv6rlOJ_FqTCcbRzXXaC3C9hWNAyVf_rvjMfZTnZ2wK6wFMXEUD2NLaXRvT9q3RTaK7v_JDiIaIvWaboP1EVp9CaPTA8rYfHvco3_XW626nnwJl5tRpZvR0O64hwV4a8z0Swbl5enkPvxWAnT44wdJBFyh_k8TseMCzNiKe3LgW9eJMoQsaHXwuhHR6hE9z2IK-ZTPVa-oR_K7-l_3EqYngB6llfbiLIYditaVDu-jurGQmC0rkJaGztFuC9V4glvPNWfscCZ_y9eOwPb2Liz-wDTTcbGLUs4zCWHebTWfoc_zGCmdR8vaAQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FFsPalm%3Fhighlight%3D%2528PALM%2529),
>> and I copied fspalm, mri_volcluster, and mri_surfcluster into
>> $FREESURFER_HOME/bin. But get error: MRISread(): could not open file
>> mri_surfcluster: could not read surface
>> /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
>> Reading source surface
>> /home/lipalab/Desktop/hwj/GLM/children/fsaverage/surf/lh.white
>> And after I copy mri_volcluster, and mri_surfcluster into
>> $FREESURFER_HOME/bin, I got this error when I run mri_glmfit-sim.
>> I wonder if it's because of my freesurfer's version? And if it works for
>> me if I get a newer version, will it be ok if I recon-all, mri_glm-stim,
>> mri_glmfit-sim on 6.0v and do the fspalm on 7.2v within one project?
>>
>> I've searched the list and no similar errors have been reported. Does
>> anyone have any thoughts on how to trouble-shoot this one? Also, I've
>> attached the fspalm.log and in case it's of any use.
>>
>> 1) FreeSurfer version: 
>> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1-f53a55a
>>
>> 2) Platform: Ubuntu 18.04 LTS(Bionic Beaver)
>>
>> 3) uname -a: Linux lipalab-Precision-5820-Tower 5.4.0-100-generic 
>> #113~18.04.1-Ubuntu SMP Mon Feb 7 15:02:59 UTC 2022 x86_64 x86_64 x86_64 
>> GNU/Linux
>>
>> 4) fspalm.log and perm.th40.abs.mri_glmfit-sim.log: see attached
>>
>>
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Please note that this e-mail is not secure (encrypted).  If you do not wish to 
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