[Freesurfer] Error with mris_convert

2021-04-25 Thread バキット・ムダシル 
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Hi, 
I manually made annotation files on an inflated surface of 40 subjects. The 
labels that makes these annotfiles are 13 in total but not present in all 
subjects every time, some can be missing depending on the brains surface 
morphology. I made the ctab files manually in the label folder in eluding an 
unknown label in the first line. I tried to convert one of the annotfiles into 
gii format and got the following error:
 mris_convert --annot $SUBJECTS_DIR/spl_01/label/lh.par.annot 
$SUBJECTS_DIR/spl_01/surf/lh.white ~/Desktop/spl_01/lh.par.gii
reading colortable from annotation file...
colortable with 14 entries read (originally none)
Segmentation fault: 11

What this error exactly means, and how I can solve this issue. 
Thanks

Mudathir





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Re: [Freesurfer] mris_average_surface fails

2021-04-18 Thread バキット・ムダシル 
External Email - Use Caution

Thanks Douglas. 
Here what happened. I did as you said and moved the $SUBJECTS_DIR out of the 
/Applications folder to somewhere in my home folder. Still the same error. But 
when I did ran the command through freesurfer 6 it worked fine even in the 
/Applications folder. Also, a freesurfer 7 in an Ubuntu virtual machine worked 
fine. So I think it has to do with something in the freesurfer 7.1.1 version I 
have in my computer.

I would like to add a question if you don’t mind. Since I found here in the 
forum that the average is in the MNI305 space, how I can make an average of my 
sample in MNI152 space from the start?

Thanks

Mudathir


> On Apr 14, 2021, at 23:26, Douglas N. Greve  wrote:
> 
> It looks like you do there, but downstream you might not. In general, macs 
> don't like to give you permission in the apps folder. Try pointer your 
> SUBJECTS_DIR to another location, eg, in your home directory
> 
> On 4/6/2021 8:44 PM, バキット・ムダシル wrote:
>> External Email - Use Caution
>> 
>> I Think I have a permission. I ran chmod -R u+rwX to make sure, but the 
>> error was the same. Can you confirm from below please?
>> 
>> \mudathirbakhit$ ls -l $FREESURFER_HOME/
>> total 568
>> drwxr-xr-x   39 mudathirbakhit  admin   1248 Mar 18 20:24 6.0.0
>> -rwxr-xr-x1 mudathirbakhit  wheel   3240 Aug 12  2020 ASegStatsLUT.txt
>> -rwxr-xr-x1 mudathirbakhit  wheel  47514 Aug 12  2020 DefectLUT.txt
>> -rwxr-xr-x@   1 mudathirbakhit  wheel  89181 Aug 12  2020 
>> FreeSurferColorLUT.txt
>> -rwxr-xr-x1 mudathirbakhit  wheel  18152 Aug 12  2020 FreeSurferEnv.csh
>> -rwxr-xr-x1 mudathirbakhit  wheel  18223 Aug 12  2020 FreeSurferEnv.sh
>> drwxrwxr-x@   3 mudathirbakhit  wheel 96 Mar 16 13:11 Freeview.app
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 10:06 Freeview_backup.app
>> -rwxr-xr-x@   1 mudathirbakhit  wheel  28381 Aug 12  2020 SegmentNoLUT.txt
>> -rwxr-xr-x1 mudathirbakhit  wheel   1358 Aug 12  2020 SetUpFreeSurfer.csh
>> -rwxr-xr-x1 mudathirbakhit  wheel   1350 Aug 12  2020 SetUpFreeSurfer.sh
>> -rwxr-xr-x@   1 mudathirbakhit  wheel   4104 Aug 12  2020 
>> Simple_surface_labels2009.txt
>> -rwxr-xr-x1 mudathirbakhit  wheel  25476 Aug 12  2020 WMParcStatsLUT.txt
>> -rw-r--r--@   1 mudathirbakhit  staff   2718 Apr  1 14:13 aparc+aseg.txt
>> drwxr-xr-x  126 mudathirbakhit  wheel   4032 Apr  7 07:22 average
>> drwxr-xr-x  766 mudathirbakhit  wheel  24512 Mar 17 10:06 bin
>> -rwxr-xr-x1 mudathirbakhit  wheel 47 Aug 12  2020 build-stamp.txt
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 19:35 color
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 diffusion
>> drwxr-xr-x   37 mudathirbakhit  wheel   1184 Aug 12  2020 docs
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 etc
>> drwxr-xr-x5 mudathirbakhit  wheel160 Aug 12  2020 fsafd
>> drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 fsfast
>> drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 lib
>> -rw-r--r--@   1 mudathirbakhit  wheel 55 Feb 17 09:40 license.txt
>> drwxr-xr-x  185 mudathirbakhit  wheel   5920 Apr  7 07:22 matlab
>> drwxr-xr-x   11 mudathirbakhit  wheel352 Apr  7 07:22 mni
>> -rw-r--r--@   1 mudathirbakhit  staff641 Apr  6 16:13 par.txt
>> drwxr-xr-x8 mudathirbakhit  wheel256 Apr  7 07:22 python
>> drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 sessions
>> -rwxr-xr-x1 mudathirbakhit  wheel134 Aug 12  2020 sources.csh
>> -rwxr-xr-x1 mudathirbakhit  wheel132 Aug 12  2020 sources.sh
>> drwxr-xr-x+  42 mudathirbakhit  wheel   1344 Apr  7 09:37 subjects
>> -rwxr-xr-x1 mudathirbakhit  wheel   1681 Aug 12  2020 
>> tkmeditParcColorsCMA
>> drwxr-xr-x   38 mudathirbakhit  wheel   1216 Apr  7 07:22 trctrain
>> -rwxr-xr-x    1 mudathirbakhit  wheel972 Aug 12  2020 uninstall.sh
>> 
>>> On Apr 6, 2021, at 22:30, Douglas N. Greve >> <mailto:dgr...@mgh.harvard.edu>> wrote:
>>> 
>>> Do you have write permissions to
>>> 
>>> /Applications/freesurfer/subjects
>>> 
>>> Of not on a mac
>>> 
>>> On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
>>>> External Email - Use Caution
>>>> 
>>>> Hi,
>>>> I am trying to make an average subject but when the process reaches 
>>>> mris_average_surface it fails as seen below.
>>>> My command was as follow:
>>>> make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 
>>>> spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl

Re: [Freesurfer] Tract endpoint density map surface overlay

2021-04-16 Thread バキット・ムダシル 
External Email - Use Caution

Hi, Anastasia. Thanks a lot. Sure I will try your suggestions.

Mudathir

> On Mar 31, 2021, at 13:00, Yendiki, Anastasia  
> wrote:
> 
> Hi Mudathir - There are several ways to configure the projection from the 
> volume to the surface, so you might want to look at the options of 
> mri_vol2surf to make sure that it's doing exactly what you want. There are 
> ways to control how deep you go from the surface (projfrac/projdist) and ways 
> to control what quantity you extract from the volume voxels along that depth 
> (avg/max). It also gives you the option to smooth the points in the volume 
> before projecting or on the surface after projecting. You can play with these 
> things to change the appearance of the end result.
> 
> Anastasia.
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> 
>  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of バキット・ムダシル 
> mailto:m-bak...@fmu.ac.jp>>
> Sent: Tuesday, March 30, 2021 11:02 PM
> To: Freesurfer support list  <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] Tract endpoint density map surface overlay
>  
> External Email - Use Caution
> Hi everyone,
> 
> I need to confirm if the steps below are correct, so I would like to ask 
> freesurfer experts help. By using the Left-Cerebral-White-Matter mask 
> imported from freesurfer as a seed I created a tract end points density image 
> of the arcuate fasciculus in a NIFTI format (first figure). I want to display 
> the image on the same subject’s white matter surface. So, I wrote the command 
> as follows 
> 
> 
> mri_vol2surf --src DensityMAP.nii.gz --out filename.mgh --hemi lh --surf 
> white --out_type mgh --regheader subject_id
> 
> The output as seen in the second figure. 
> 
> Thanks 
> 
> Mudathir
> 
> 
> 
> 
> 
> 
> 
> ___
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>  
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[Freesurfer] The cvs_avg35

2021-04-14 Thread バキット・ムダシル 
External Email - Use Caution

Hi,
I was looking for any document describes how the cvs_avg35 and 
cvs_avg35_inMNI152 were made? Can you please send me a link or give me a brief 
about it please? I searched in the freesurfer wiki and here in the freesurfer 
folder but no success.
Also, I found from literature that the fsaverage was made from a data of 40 
subjects that includes 10 cases of Alzheimer disease. Can I ask what was the 
reason to include those 10 cases to create this template?

Thanks

Mudathir





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Re: [Freesurfer] mris_average_surface fails

2021-04-06 Thread バキット・ムダシル 
External Email - Use Caution

I Think I have a permission. I ran chmod -R u+rwX to make sure, but the error 
was the same. Can you confirm from below please?

\mudathirbakhit$ ls -l $FREESURFER_HOME/
total 568
drwxr-xr-x   39 mudathirbakhit  admin   1248 Mar 18 20:24 6.0.0
-rwxr-xr-x1 mudathirbakhit  wheel   3240 Aug 12  2020 ASegStatsLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel  47514 Aug 12  2020 DefectLUT.txt
-rwxr-xr-x@   1 mudathirbakhit  wheel  89181 Aug 12  2020 FreeSurferColorLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel  18152 Aug 12  2020 FreeSurferEnv.csh
-rwxr-xr-x1 mudathirbakhit  wheel  18223 Aug 12  2020 FreeSurferEnv.sh
drwxrwxr-x@   3 mudathirbakhit  wheel 96 Mar 16 13:11 Freeview.app
drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 10:06 Freeview_backup.app
-rwxr-xr-x@   1 mudathirbakhit  wheel  28381 Aug 12  2020 SegmentNoLUT.txt
-rwxr-xr-x1 mudathirbakhit  wheel   1358 Aug 12  2020 SetUpFreeSurfer.csh
-rwxr-xr-x1 mudathirbakhit  wheel   1350 Aug 12  2020 SetUpFreeSurfer.sh
-rwxr-xr-x@   1 mudathirbakhit  wheel   4104 Aug 12  2020 
Simple_surface_labels2009.txt
-rwxr-xr-x1 mudathirbakhit  wheel  25476 Aug 12  2020 WMParcStatsLUT.txt
-rw-r--r--@   1 mudathirbakhit  staff   2718 Apr  1 14:13 aparc+aseg.txt
drwxr-xr-x  126 mudathirbakhit  wheel   4032 Apr  7 07:22 average
drwxr-xr-x  766 mudathirbakhit  wheel  24512 Mar 17 10:06 bin
-rwxr-xr-x1 mudathirbakhit  wheel 47 Aug 12  2020 build-stamp.txt
drwxr-xr-x3 mudathirbakhit  wheel 96 Mar 17 19:35 color
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 diffusion
drwxr-xr-x   37 mudathirbakhit  wheel   1184 Aug 12  2020 docs
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 etc
drwxr-xr-x5 mudathirbakhit  wheel160 Aug 12  2020 fsafd
drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 fsfast
drwxr-xr-x6 mudathirbakhit  wheel192 Apr  7 07:22 lib
-rw-r--r--@   1 mudathirbakhit  wheel 55 Feb 17 09:40 license.txt
drwxr-xr-x  185 mudathirbakhit  wheel   5920 Apr  7 07:22 matlab
drwxr-xr-x   11 mudathirbakhit  wheel352 Apr  7 07:22 mni
-rw-r--r--@   1 mudathirbakhit  staff641 Apr  6 16:13 par.txt
drwxr-xr-x8 mudathirbakhit  wheel256 Apr  7 07:22 python
drwxr-xr-x3 mudathirbakhit  wheel 96 Aug 12  2020 sessions
-rwxr-xr-x1 mudathirbakhit  wheel134 Aug 12  2020 sources.csh
-rwxr-xr-x1 mudathirbakhit  wheel132 Aug 12  2020 sources.sh
drwxr-xr-x+  42 mudathirbakhit  wheel   1344 Apr  7 09:37 subjects
-rwxr-xr-x1 mudathirbakhit  wheel   1681 Aug 12  2020 tkmeditParcColorsCMA
drwxr-xr-x   38 mudathirbakhit  wheel   1216 Apr  7 07:22 trctrain
-rwxr-xr-x1 mudathirbakhit  wheel972 Aug 12  2020 uninstall.sh

> On Apr 6, 2021, at 22:30, Douglas N. Greve  wrote:
> 
> Do you have write permissions to
> 
> /Applications/freesurfer/subjects
> 
> Of not on a mac
> 
> On 4/6/2021 6:39 AM, バキット・ムダシル wrote:
>> External Email - Use Caution
>> 
>> Hi,
>> I am trying to make an average subject but when the process reaches 
>> mris_average_surface it fails as seen below.
>> My command was as follow:
>> make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 
>> spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
>> Can you please guide me to solve this issue.
>> 
>> Thanks
>> 
>> Mudathir
>> 
>> ###
>> #@# Making average lh.white surface -
>> Tue Apr  6 19:23:39 JST 2021
>> /Applications/freesurfer/subjects/avgsubject
>> mris_make_average_surface -i 7 -o white -sdir-out 
>> /Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 
>> spl_02 spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
>> reading vertex positions from white...
>> ---
>> hemi= lh
>> avg_surf_name   = white
>> canon_surf_name = sphere.reg
>> out_sname   = avgsubject
>> xform   = talairach.xfm
>> ---
>> 
>> 
>> Is a directory
>> Is a directory
>> ERROR: creating directory /
>> ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf
>> mris_average_surface failed
>> ERROR: make_average_surface
>> #
>> 
>> 
>> 
>> 
>> 
>> 
>> ___
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[Freesurfer] mris_average_surface fails

2021-04-06 Thread バキット・ムダシル 
External Email - Use Caution

Hi,
I am trying to make an average subject but when the process reaches 
mris_average_surface it fails as seen below.
My command was as follow:
make_average_subject --out avgsubject --subjects spl_01 spl_02 spl_03 spl_04 
spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
Can you please guide me to solve this issue.

Thanks

Mudathir

###
#@# Making average lh.white surface -
Tue Apr  6 19:23:39 JST 2021
/Applications/freesurfer/subjects/avgsubject
mris_make_average_surface -i 7 -o white -sdir-out 
/Applications/freesurfer/subjects lh white sphere.reg avgsubject spl_01 spl_02 
spl_03 spl_04 spl_05 spl_06 spl_07 spl_08 spl_09 spl_10
reading vertex positions from white...
---
hemi= lh
avg_surf_name   = white
canon_surf_name = sphere.reg
out_sname   = avgsubject
xform   = talairach.xfm
---


Is a directory
Is a directory
ERROR: creating directory /
ERROR: creating directory /Applications/freesurfer/subjects/avgsubject/surf
mris_average_surface failed
ERROR: make_average_surface
#






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Re: [Freesurfer] equivolumetric surfaces

2021-03-20 Thread バキット・ムダシル 
External Email - Use Caution

Sure, I will give it a try. Thanks Matt.

Mudathir



> On Mar 19, 2021, at 22:25, Glasser, Matthew  wrote:
> 
> External Email - Use Caution
> 
> 
> You can do this with Connectome Workbench command (wb_command -surface-layer 
> and wb_command -volume-to-surface-mapping).
>  
> Matt.
>  
> From:  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of バキット・ムダシル 
> mailto:m-bak...@fmu.ac.jp>>
> Reply-To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Friday, March 19, 2021 at 2:21 AM
> To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] equivolumetric surfaces
> External Email - Use Caution
> Dear freesurfer experts, 
>  
> I want to create an equivolumetric surfaces (using the tool from: MailScanner 
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
> be 
> https://secure-web.cisco.com/1O7fxeb8WB8OcnE6l4q1HALvLzu_CCGz5dWKgk0QgGYvKzrQ9S096mvJCiLTPlywS0MlK_wopxltBaPMu2QTllvkKmYTor-D_Lns3XuUXc6ob1PtIwIyi80g3z0vay_oCK8Dy66cCZRfl5NW4Zn2EqQjpLajNfUb5Q6t9QWHwch64Lfc1ZoLYqXH1aZwCRGm7CGLajgSsQ32qhNKbAXQ3n-3Y6V8tz4bZpPZJl-qkgDHRc691v92itvWYZ7MQ9GrYOmAJ5MrBmqxGdtLheJA2Hg/https%3A%2F%2Fgithub.com%2Fkwagstyl%2Fsurface_tools
>  
> <https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1eoOQXja0KaogvHBx39bkqpnP1Qnz5FuZhT-DTLRXZLIQWp64WXTSgyrwspQMNHWCVzQPv1cqguMDF7AiGzYh01WxTW7m8FHiaJUhjGnV4OUOHBvBdP7TEBNSTE-wITBcBhQio6M-0BWoLcRMIE8ov3uosoZa-RneDMp9tALUDf97709r5pZLfXcySduo0v7WZYNjE9grdo_LK1JjVuAC/https%3A%2F%2Fgithub.com%2Fkwagstyl%2Fsurface_tools>)
>  and to sample the intensities of the T1wDividedByT2w volume at all the 
> depths. I created the surfaces and after running the mri_vol2surf command I 
> faced the error below. I don’t know why the path to the surface is not 
> correct. I tried it in different devices with different versions of 
> freesurfer but the results were the same. Any idea what I did wrong? Thanks
>  
> Mudathir
>  
> #
>  freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/7.1.1
> FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
> MNI_DIR   /Applications/freesurfer/7.1.1/mni
> FSL_DIR   /usr/local/fsl
> mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
> --out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
> $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
> srcvol = 
> /Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Computing registration from header.
>   Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
> reference.
>  original matrix ---
>  1.0   0.0   0.0   0.0;
>  0.0   0.0   1.0   0.0;
>  0.0  -1.0   0.0   0.35001;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> Reading surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> error: No such file or directory
> error: 
> MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
>  could not open file
> error: No such file or directory
> error: mri_vol2surf: could not read surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> mudathirbakhit%
> #
>  
> 
>  
> 
>  
> The materials in this message are private and may contain Protected 
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Re: [Freesurfer] equivolumetric surfaces

2021-03-20 Thread バキット・ムダシル 
External Email - Use Caution

Thanks Bruce!

Mudathir






> On Mar 20, 2021, at 1:07, Fischl, Bruce  wrote:
> 
> HI Mudathir
>  
> Looks like mri_vol2surf doesn’t want the full path in the “surf” parameter – 
> just stuff after the “lh.”.
>  
> Cheers
> Bruce
>  
> From: freesurfer-boun...@nmr.mgh.harvard.edu 
>  
>  > On Behalf Of ·
> Sent: Friday, March 19, 2021 2:21 AM
> To: freesurfer@nmr.mgh.harvard.edu 
> Subject: [Freesurfer] equivolumetric surfaces
>  
> External Email - Use Caution
> 
> Dear freesurfer experts,
>  
> I want to create an equivolumetric surfaces (using the tool from: MailScanner 
> has detected a possible fraud attempt from "secure-web.cisco.com" claiming to 
> be 
> https://secure-web.cisco.com/1q5cs6Q_ZjnLHZkjjEuUs4b1u23XY86a8gNRMaeFgH_N3J6JICUha47j_o_aD2q7QRhSc13qe9vJaiojvYmyb2s5pdCeKakYIGzkOczT8cZdVK8jE0wOP21LYDW_YDEuSFfh1fQBc-LgPaaR8tNdoTZO1A78ULqlJm2J5uxFLwoVY0h2rjV9LdP_-hWBSZe5W7SYS5n7UOfR3IS2bIBc5OwPtyxpHqYK3q9HZ3e78zAODwAXNDKO03VMN1K08oRVuqNXu6CxlbWI624ePQ19RkQ/https%3A%2F%2Fgithub.com%2Fkwagstyl%2Fsurface_tools
>  
> )
>  and to sample the intensities of the T1wDividedByT2w volume at all the 
> depths. I created the surfaces and after running the mri_vol2surf command I 
> faced the error below. I don’t know why the path to the surface is not 
> correct. I tried it in different devices with different versions of 
> freesurfer but the results were the same. Any idea what I did wrong? Thanks
>  
> Mudathir
>  
> #
>  freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
> Setting up environment for FreeSurfer/FS-FAST (and FSL)
> FREESURFER_HOME   /Applications/freesurfer/7.1.1
> FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
> FSF_OUTPUT_FORMAT nii.gz
> SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
> MNI_DIR   /Applications/freesurfer/7.1.1/mni
> FSL_DIR   /usr/local/fsl
> mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
> --out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
> $SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
> srcvol = 
> /Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
> srcreg unspecified
> srcregold = 0
> srcwarp unspecified
> surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> hemi = lh
> reshape = 0
> interp = nearest
> float2int = round
> GetProjMax = 0
> INFO: float2int code = 0
> Done loading volume
> Computing registration from header.
>   Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
> reference.
>  original matrix ---
>  1.0   0.0   0.0   0.0;
>  0.0   0.0   1.0   0.0;
>  0.0  -1.0   0.0   0.35001;
>  0.0   0.0   0.0   1.0;
>  original matrix ---
> Reading surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> error: No such file or directory
> error: 
> MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
>  could not open file
> error: No such file or directory
> error: mri_vol2surf: could not read surface 
> /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
> mudathirbakhit%
> #
>  
> 
>  
> ___
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>  
>

[Freesurfer] equivolumetric surfaces

2021-03-19 Thread バキット・ムダシル 
External Email - Use Caution

Dear freesurfer experts,

I want to create an equivolumetric surfaces (using the tool from: 
https://secure-web.cisco.com/1RxQBNBh7QLlgBP46WWIONAGLCrtuooPBalXpNMTOlsF1eoOQXja0KaogvHBx39bkqpnP1Qnz5FuZhT-DTLRXZLIQWp64WXTSgyrwspQMNHWCVzQPv1cqguMDF7AiGzYh01WxTW7m8FHiaJUhjGnV4OUOHBvBdP7TEBNSTE-wITBcBhQio6M-0BWoLcRMIE8ov3uosoZa-RneDMp9tALUDf97709r5pZLfXcySduo0v7WZYNjE9grdo_LK1JjVuAC/https%3A%2F%2Fgithub.com%2Fkwagstyl%2Fsurface_tools
 
)
 and to sample the intensities of the T1wDividedByT2w volume at all the depths. 
I created the surfaces and after running the mri_vol2surf command I faced the 
error below. I don’t know why the path to the surface is not correct. I tried 
it in different devices with different versions of freesurfer but the results 
were the same. Any idea what I did wrong? Thanks

Mudathir

#
 freesurfer-darwin-macOS-7.1.1-20200811-8b40551 
Setting up environment for FreeSurfer/FS-FAST (and FSL)
FREESURFER_HOME   /Applications/freesurfer/7.1.1
FSFAST_HOME   /Applications/freesurfer/7.1.1/fsfast
FSF_OUTPUT_FORMAT nii.gz
SUBJECTS_DIR  /Applications/freesurfer/7.1.1/subjects
MNI_DIR   /Applications/freesurfer/7.1.1/mni
FSL_DIR   /usr/local/fsl
mudathir% mri_vol2surf --src $SUBJECTS_DIR/spl_01/mri/T1wDividedByT2w.nii.gz 
--out $SUBJECTS_DIR/spl_01/lh.equi_intensity_1.0.mgh --hemi lh --surf 
$SUBJECTS_DIR/spl_01/surf/lh.equi1.0.pial --out_type mgh --regheader spl_01
srcvol = 
/Applications/freesurfer/7.1.1/subjects/spl_01/mri/T1wDividedByT2w.nii.gz
srcreg unspecified
srcregold = 0
srcwarp unspecified
surf = /Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
hemi = lh
reshape = 0
interp = nearest
float2int = round
GetProjMax = 0
INFO: float2int code = 0
Done loading volume
Computing registration from header.
  Using /Applications/freesurfer/7.1.1/subjects/spl_01/mri/orig.mgz as target 
reference.
 original matrix ---
 1.0   0.0   0.0   0.0;
 0.0   0.0   1.0   0.0;
 0.0  -1.0   0.0   0.35001;
 0.0   0.0   0.0   1.0;
 original matrix ---
Reading surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
error: No such file or directory
error: 
MRISread(/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial):
 could not open file
error: No such file or directory
error: mri_vol2surf: could not read surface 
/Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh./Applications/freesurfer/7.1.1/subjects/spl_01/surf/lh.equi1.0.pial
mudathirbakhit%
#



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Re: [Freesurfer] Meylin overlay

2021-03-17 Thread バキット・ムダシル 
External Email - Use Caution

Yes. After I updated the freeview it worked! Thanks a lot Matt.

Mudathir






> On Mar 17, 2021, at 11:49, Glasser, Matthew  wrote:
> 
> External Email - Use Caution
> 
> 
> There is a bug in Freeview, I believe it has been fixed in the dev build.
>  
> Matt.
>  
> From:  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of バキット・ムダシル 
> mailto:m-bak...@fmu.ac.jp>>
> Reply-To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Tuesday, March 16, 2021 at 10:38 PM
> To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: Re: [Freesurfer] Meylin overlay
>  
> External Email - Use Caution
> Thanks Matt. I tried it with version 7.1.1 of freesurfer didn’t work but 
> worked fine with freesurfer 6. With version 7.1 it failed to load the gii 
> file. Any idea how to fix it?
>  
> Mudathir
>  
>  
>  
> 
> 
> 
>> On Mar 16, 2021, at 21:08, Glasser, Matthew > <mailto:glass...@wustl.edu>> wrote:
>>  
>> External Email - Use Caution
>>  
>> You should be able to load files like 
>> ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii
>>  in Freeview.
>> 
>> Matt.
>>  
>> From: > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of バキット・ムダシル 
>> mailto:m-bak...@fmu.ac.jp>>
>> Reply-To: Freesurfer support list > <mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Date: Monday, March 15, 2021 at 10:18 PM
>> To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" 
>> mailto:freesurfer@nmr.mgh.harvard.edu>>
>> Subject: [Freesurfer] Meylin overlay
>>  
>> External Email - Use Caution
>> Dear freesurfer experts,
>>  
>> Is there a way to import the individual surface myelin maps from the human 
>> connectome project database to freesurfer and use them as overlays? Or can 
>> we create them in freesurfer?
>>  
>> Mudathir
>>  
>>  
>>  
>>  
>> 
>>  
>>  
>>  
>> The materials in this message are private and may contain Protected 
>> Healthcare Information or other information of a sensitive nature. If you 
>> are not the intended recipient, be advised that any unauthorized use, 
>> disclosure, copying or the taking of any action in reliance on the contents 
>> of this information is strictly prohibited. If you have received this email 
>> in error, please immediately notify the sender via telephone or return mail.
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>> MailScanner has detected a possible fraud attempt from 
>> "secure-web.cisco.com" claiming to 
>> behttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 
>> <https://secure-web.cisco.com/1dVyyIVOL4vUyrUJnnyD5dKmi7hFYV2vkiJm8YkOpaSoUJtUrZUhJkzn_Vyu4jjgR66BUATSUNxEuPP1slYgmzRF0h2aCbtsHujvj-8_gLa5GbJviT_bDBo82N2AHNv0ECL07qpGfwA1bREYDl8ymRlISm9o0_YSJjENL1fcxNyb1BXkiEZVKlny0h-XAVgTVWWOM0p-gMxWxM_xlvrWoy8GPir3sfx7_3i1n0MIAMn54ma2Hp3lD_ubO1bVltzsRWS0DbE2J0bWGHSg8kr1H4A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
>  
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> ___
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> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
> https://secure-web.cisco.com/1I_3qZceVN8ce9ZoKkPNUr42OpjMGTB48QsX25DlrCyJ3bNpJrI3yD8Zp3kv2pO5S9qjQSCfenUzwcCfRmY-esa091xs4ZT9m9L6XOa34iPT11vVRsYjk1BmBQArEk31y1oMIPj09Y82Zzs_hTVqOp36otWKbPAQrkdwMgoIYYj9D0vHKTaSsBXaNAIRHT75-L2Grt4ZTR1WTs___ipOGMniRbnRNAIXsT380rOyQRX2PSkt-V_SpptGo6RzIingAxqK4pTAKMQvjUTuqgwhGiA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
>  
> <https://secure-web.cisco.com/1I_3qZceVN8ce9ZoKkPNUr42OpjMGTB48QsX25DlrCyJ3bNpJrI3yD8Zp3kv2pO5S9qjQSCfenUzwcCfRmY-esa091xs4ZT9m9L6XOa34iPT11vVRsYjk1BmBQArEk31y1oMIPj09Y82Zzs_hTVqOp36otWKbPAQrkdwMgoIYYj9D0vHKTaSsBXaNAIRHT75-L2Grt4ZTR1WTs___ipOGMniRbnRNAIXsT380rOyQRX2PSkt-V_SpptGo6RzIingAxqK4pTAKMQvjUTuqgwhGiA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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Re: [Freesurfer] Meylin overlay

2021-03-16 Thread バキット・ムダシル 
External Email - Use Caution

Thanks Matt. I tried it with version 7.1.1 of freesurfer didn’t work but worked 
fine with freesurfer 6. With version 7.1 it failed to load the gii file. Any 
idea how to fix it?

Mudathir





> On Mar 16, 2021, at 21:08, Glasser, Matthew  wrote:
> 
> External Email - Use Caution
> 
> 
> You should be able to load files like 
> ${StudyFolder}/${Subject}/MNINonLinear/Native/${Subject}.${Hemisphere}.MyelinMap[_BC].native.func.gii
>  in Freeview.
> 
> Matt.
>  
> From:  <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of バキット・ムダシル 
> mailto:m-bak...@fmu.ac.jp>>
> Reply-To: Freesurfer support list  <mailto:freesurfer@nmr.mgh.harvard.edu>>
> Date: Monday, March 15, 2021 at 10:18 PM
> To: "freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu>" 
> mailto:freesurfer@nmr.mgh.harvard.edu>>
> Subject: [Freesurfer] Meylin overlay
>  
> External Email - Use Caution
> Dear freesurfer experts,
>  
> Is there a way to import the individual surface myelin maps from the human 
> connectome project database to freesurfer and use them as overlays? Or can we 
> create them in freesurfer?
>  
> Mudathir
>  
>  
>  
>  
> 
>  
> 
>  
> The materials in this message are private and may contain Protected 
> Healthcare Information or other information of a sensitive nature. If you are 
> not the intended recipient, be advised that any unauthorized use, disclosure, 
> copying or the taking of any action in reliance on the contents of this 
> information is strictly prohibited. If you have received this email in error, 
> please immediately notify the sender via telephone or return mail.
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
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>  
> <https://secure-web.cisco.com/1dVyyIVOL4vUyrUJnnyD5dKmi7hFYV2vkiJm8YkOpaSoUJtUrZUhJkzn_Vyu4jjgR66BUATSUNxEuPP1slYgmzRF0h2aCbtsHujvj-8_gLa5GbJviT_bDBo82N2AHNv0ECL07qpGfwA1bREYDl8ymRlISm9o0_YSJjENL1fcxNyb1BXkiEZVKlny0h-XAVgTVWWOM0p-gMxWxM_xlvrWoy8GPir3sfx7_3i1n0MIAMn54ma2Hp3lD_ubO1bVltzsRWS0DbE2J0bWGHSg8kr1H4A/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer>
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[Freesurfer] Meylin overlay

2021-03-15 Thread バキット・ムダシル 
External Email - Use Caution

Dear freesurfer experts,

Is there a way to import the individual surface myelin maps from the human 
connectome project database to freesurfer and use them as overlays? Or can we 
create them in freesurfer?

Mudathir






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[Freesurfer] VB password

2021-02-17 Thread バキット・ムダシル 
External Email - Use Caution

Hi, I am attempting to run the Freesurfer Ubuntu virtual box but I need the 
“Developed” password.  Is it possible to have it?

Best

Mudathir

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