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Today's Topics:
1. Re: Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed} (???)
2. Re: tkregister issue with reg-feat2anat {Disarmed}
(Douglas N. Greve)
3. Re: Extract he value of area and volume in the fsaverage for
every subject {Disarmed} {Disarmed} {Disarmed} {Disarmed}
(Douglas N. Greve)
4. Re: Sulc maps (Douglas N. Greve)
5. Re: Help with MRI labels (Douglas N. Greve)
6. mris_pmake error - freadFloat: fread failed (Nasr, Shahin,Ph.D.)
7. Support: Password Request for Ubuntu_710 to download
Freesurfer on Windows 10 {Disarmed} (Park, James)
8. Re: Support: Password Request for Ubuntu_710 to download
Freesurfer on Windows 10 {Disarmed} {Disarmed} (fsbuild)
9. Re: Help with MRI labels {Disarmed} (Alberto Del Cerro Leon)
----------------------------------------------------------------------
Message: 1
Date: Thu, 12 Nov 2020 18:39:44 +0800 (GMT+08:00)
From: ??? <mengjun@csu.edu.cn>
Subject: Re: [Freesurfer] Extract he value of area and volume in the
fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}
{Disarmed}
To: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6071ada5.3fd7.175bc0a2c24.Coremail.mengjun@csu.edu.cn>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Thank you very much, I get lh_areapial.avgwf.dat and lh_areapial.sum file after the mri_segstats command
(1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
(2) When I extract the volumes, the lh_volume.sum displays the unit for the volume is Area_mm2?Blue color). Is this correct?
ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range
1 0 161058 81037.1 Seg0000 242940.3281 0.7312 0.0000 3.8885 3.8885
2 1 2784 1182.3 Seg0001 3760.6619 0.2525 0.7136 1.8140 1.1005
Following is the code for extracting volumes
mri_segstats
--i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.volume.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_volume.avgwf.dat (output file)
--accumulate
--sum lh_volume.sum (output file)
-----????-----
???:"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
????:2020-11-11 23:58:20 (???)
???: freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}
Sorry, try this
mri_segstats
--i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
On 11/5/2020 10:26 PM, ??? wrote:
External Email - Use Caution
I tried following codes according to the suggestions, the terminal reported an error: cannot do frame average without input volume
mri_segstats
--seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel fsaverage lh lh.areapial.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
-----????-----
???:"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
????:2020-11-05 22:37:07 (???)
???:freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed} {Disarmed}
Try
--slabel fsaverage lh /path/to/lh.areapial.label
On 11/2/2020 10:24 PM, ??? wrote:
External Email - Use Caution
Thank you very much! I tried to extract the areas with the following codes:
mri_segstats
--seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
--slabel lh.areapial.label (This was the label extracted from the fsaverage after multi-correction)
--avgwf lh_areapial.avgwf.dat (output file)
--accumulate
--sum lh_areapial.sum (output file)
I did not get a text file including the areas of all subjects. Is this code correct?
-----????-----
???:"Douglas N. Greve" <dgreve@mgh.harvard.edu>
????:2020-11-02 23:36:14 (???)
???:freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject {Disarmed}
I think the reason for this may be that the data in fsaverage space (after mris_preproc) will have had a jacobian correction which will not be in data on the native surface. For this reason, I would not use #1. #2 is fine.You can apply your label in fsaverage
space to the y.mgh used as input to mri_segstats specifying the label using --slabel and using --avgwf output and also use --accumulate; run it with --help for more info. This will create a text file of the areas or volumes (depending upon which y.mgh you
input) all your subjects for that label.
On 10/30/2020 10:37 PM, ??? wrote:
External Email - Use Caution
Dear Professors:
I compared the thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found statistic difference region in the cortex area, volume respectively. I defined the statistic difference regions as a label on the
fsaverage and mapped this label to subjects by Qdec/mri_label2label. The label defined on the fsaverage was mapped onto all subjects successfully, and the label in subjects matched well with the inflated cortex of subjects in Freeview Then the value of the
label in every single subjects was extracted, and I found that there is no statistic difference in the value regarding to the area and volume between the mild traumatic brain injury patients and health control subjects. Following are my questions:
(1)Can I carry out correlation analysis between the cortex area and volume with the behavior scores through these non-statistical extracted values?
(2)Can I extract the value of cortex area and volume in the standard space for every TBI and health control subjects, and carry out correlation analysis between the cortex area and volume with the behavior scores. How can I extract the value of cortex area
and volume in the standard space for every TBI and health control subjects
Best wishes
Mengjun Li
-----????-----
???:"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
????:2020-10-30 23:40:30 (???)
???:freesurfer@nmr.mgh.harvard.edu
??:
??: Re: [Freesurfer] Extract he value of area and volume in the fsaverage for every subject
Do you mean you compared your TBI subjects against fsaverage? That is not proper methodology.
On 10/29/2020 9:51 PM, ??? wrote:
External Email - Use Caution
Dear FreeSurfer Developers:
I compared the cortical thickness, area, volume in the mild traumatic brain injury patients with health control by FreeSurFer, and found a statistic difference region in the cortex area and volume after correction. How can I extract the value of cortex area
and volume for every subject in the fsaverage with the code of mri_segstats
FreeSurfer version: freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform: macOS High Sierra.
Best wishes
Mengjun Li
Second Xiangya Hospital
Central South University
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------------------------------
Message: 2
Date: Thu, 12 Nov 2020 09:19:05 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] tkregister issue with reg-feat2anat
{Disarmed}
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <6c5ad2e8-4cce-0bb2-29f8-8158fdc4a068@mgh.harvard.edu>
Content-Type: text/plain; charset="windows-1252"
Nope, that's a bug. I've attached a new version. Copy and make it executable
cp $FREESURFER_HOME/bin
chmod a+x $FREESURFER_HOME/bin/reg-feat2anat
Then try again
On 11/11/2020 11:55 PM, Walsh, Erin wrote:
>
> ????????External Email - Use Caution
>
> Greetings,
>
> I am experiencing a similar tkregister2 issue described in this thread
> when attempting to run reg-feat2anat: *MailScanner has detected a
> possible fraud attempt from "secure-web.cisco.com" claiming to be*
>
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/msg68229.html
> <
https://secure-web.cisco.com/1H9mU-9s00zN3P3mT0enoWLpI-9zwcO9lCds21sBQW9qoSPpMEcJ1KDcbQsvZ9iZ1Wu8IP-mx8SyKgy5jTrUhqaifkxwjnbydCn313Or34EBuAeIPcKmXUV4FKIUHu40DO-K4tlIsBBuqJiWGQHla8aFFqx48xIcSripk-6LwN6dWCO54xxItZWbucQGSL7YHt8zMgt1Q3RkeKUYYsXeQegOqzfQRPfegNd8CP99ch-E1mhfgNf4fhJuy-83sR_XTelccCwB8_-dAqbfuF2-8SA/https%3A%2F%2Fwww.mail-archive.com%2Ffreesurfer%40nmr.mgh.harvard.edu%2Fmsg68229.html>
>
> I am using FSL version 5.0.10 and Freesurfer version 7. I have pasted
> the --debug output after my signature. I am wondering if there should
> be a call for tkregister2_cmdl_cmdl (as opposed to tkregister2_cmdl)?
>
> set TKR = tkregister2_cmdl
> set TKR = tkregister2_cmdl
> if ( $usedev ) set TKR = $DEV/$TKR/$TKR
> if ( 0 ) set TKR = /tkregister2_cmdl/tkregister2_cmdl
> if ( ! $manual ) set TKR = $TKR"_cmdl"
> if ( ! 0 ) set TKR = tkregister2_cmdl_cmdl
> set TKR = tkregister2_cmdl_cmdl
>
>
> Thank you for any help you can provide!
> Erin
> --
> Erin Walsh, Ph.D.
> Assistant Professor
> University of North Carolina-Chapel Hill
> Department of Psychiatry
> Chapel Hill, NC 27599-3367
> erin_walsh@med.unc.edu
> /pronouns: she/her/
>
>
> set echo = 1 ;
> set debug = 1 ;
> set debug = 1
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 4 != 0 )
>
> set flag = $argv[1] ; shift ;
> set flag = --feat
> shift
>
> switch ( $flag )
> switch ( --feat )
> case "--featdir":
> case --featdir:
> if ( $#argv == 0 ) goto arg1err ;
> if ( 3 == 0 ) goto arg1err
> set FeatDir = $argv[1] ; shift ;
> set FeatDir =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
> shift
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 2 != 0 )
>
> set flag = $argv[1] ; shift ;
> set flag = --subject
> shift
>
> switch ( $flag )
> switch ( --subject )
> if ( $#argv == 0 ) goto arg1err ;
> if ( 1 == 0 ) goto arg1err
> set subject = $argv[1] ; shift ;
> set subject = BA0023_V1
> shift
> breaksw
> breaksw
>
> end
> end
> while ( $#argv != 0 )
> while ( 0 != 0 )
>
> goto parse_args_return ;
> goto parse_args_return
>
>
> goto check_params ;
> goto check_params
>
> if ( $DoBBR ) then
> if ( 1 ) then
> which bbregister > /dev/null
> which bbregister
> if ( $status ) then
> if ( 0 ) then
> endif
> endif
>
> if ( $#FeatDir == 0 ) then
> if ( 1 == 0 ) then
> if ( ! -e $FeatDir ) then
> if ( ! -e
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
> ) then
> if ( ! $manual ) then
> if ( ! 0 ) then
> if ( $#subject == 0 ) then
> if ( 1 == 0 ) then
> else
> else
> if ( $?SUBJECTS_DIR == 0 ) then
> if ( 1 == 0 ) then
> if ( ! -e $SUBJECTS_DIR ) then
> if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7 ) then
> if ( ! -e $SUBJECTS_DIR/$subject ) then
> if ( ! -e /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1 ) then
> if ( $manxfm != "func2anat" && $manxfm != "std2anat" && $manxfm !=
> "func2std" ) then
> if ( func2anat != func2anat && func2anat != std2anat && func2anat !=
> func2std ) then
>
>
> goto check_params_return ;
> goto check_params_return
>
> if ( $?DEV == 0 ) set DEV = "" ;
> if ( 0 == 0 ) set DEV =
> set DEV =
>
> set TKR = tkregister2_cmdl
> set TKR = tkregister2_cmdl
> if ( $usedev ) set TKR = $DEV/$TKR/$TKR
> if ( 0 ) set TKR = /tkregister2_cmdl/tkregister2_cmdl
> if ( ! $manual ) set TKR = $TKR"_cmdl"
> if ( ! 0 ) set TKR = tkregister2_cmdl_cmdl
> set TKR = tkregister2_cmdl_cmdl
>
> set MM = mri_matrix_multiply
> set MM = mri_matrix_multiply
> if ( $usedev ) set MM = $DEV/$MM/$MM
> if ( 0 ) set MM = /mri_matrix_multiply/mri_matrix_multiply
>
> echo FeatDir is $FeatDir
> echo FeatDir is
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
> FeatDir is
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
> mkdir -p $FeatDir/reg/freesurfer/tmp
> mkdir -p
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/tmp
>
> set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat
> set exf2std_fslmat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/example_func2standard.mat
> if ( ! -e $exf2std_fslmat ) then
> if ( ! -e
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/example_func2standard.mat
> ) then
>
>
> set exfbase = $FeatDir/example_func
> set exfbase =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func
> if ( -e $exfbase.nii.gz ) then
> if ( -e
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> ) then
> setenv FSLOUTPUTTYPE NIFTI_GZ
> setenv FSLOUTPUTTYPE NIFTI_GZ
> set fslext = nii.gz ;
> set fslext = nii.gz
> endif
> endif
> if ( -e $exfbase.nii ) then
> if ( -e
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii
> ) then
> if ( -e $exfbase.img ) then
> if ( -e
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.img
> ) then
> if ( $#fslext == 0 ) then
> if ( 1 == 0 ) then
> set tempvol = $FeatDir/example_func.$fslext
> set tempvol =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> echo "template volume is $tempvol"
> echo template volume is
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> template volume is
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
>
> set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat
> set anat2exf_regdat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat
> set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat
> set anat2std_regdat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2std.register.dat
> set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat
> set std2anat_fslmat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/std2anat.fsl.mat
> set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat
> set exf2anat_init_fslmat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat
> set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat
> set exf2anat_fslmat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.fsl.mat
> set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat
> set std2exf_regdat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/std2exf.register.dat
> set exf2std_regdat = $FeatDir/reg/freesurfer/exf2std.register.dat
> set exf2std_regdat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2std.register.dat
> set segregdat = $FeatDir/reg/freesurfer/reg.bbr.dat
> set segregdat =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg.bbr.dat
> set stdbrain = $FeatDir/reg/standard.$fslext
> set stdbrain =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/standard.nii.gz
>
> set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
> set refvolcor =
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> if ( ! -e $refvolcor ) then
> if ( ! -e
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> ) then
>
>
> if ( $manual && $manxfm == func2anat ) then
> if ( 0 && func2anat == func2anat ) then
>
>
> if ( $manual && $manxfm == std2anat ) then
> if ( 0 && func2anat == std2anat ) then
>
>
> if ( $manual && $manxfm == func2std ) then
> if ( 0 && func2anat == func2std ) then
>
>
> set LF = $FeatDir/reg/freesurfer/reg-feat2anat.log
> set LF =
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> if ( -e $LF ) mv $LF $LF.bak
> if ( -e
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> ) mv
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log.bak
> echo log file is $LF
> echo log file is
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> log file is
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> date | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> date
> Wed Nov 11 18:22:53 EST 2020
> pwd | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> pwd
> /proj/dichterlab/BATA/Scripts/Hammer/Hammer_Activation/Censoring_Pipeline/Freesurfer
> echo $0 | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> echo /nas/longleaf/apps/freesurfer/7.1.0/freesurfer/bin/reg-feat2anat
> /nas/longleaf/apps/freesurfer/7.1.0/freesurfer/bin/reg-feat2anat
> echo $cmdargs | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> echo --debug --feat
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
> --subject BA0023_V1
> --debug --feat
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat
> --subject BA0023_V1
> uname -a | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> uname -a
> Linux c1125.ll.unc.edu 3.10.0-1127.19.1.el7.x86_64 #1 SMP Tue Aug 11
> 19:12:04 EDT 2020 x86_64 x86_64 x86_64 GNU/Linux
>
>
> set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
> set refvolcor =
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> if ( ! -e $refvolcor ) then
> if ( ! -e
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> ) then
>
>
>
>
> if ( $fslext == img ) then
> if ( nii.gz == img ) then
>
> mri_info --o /tmp/reg-feat2anat.rasgood.$$ --ras_good
> $FeatDir/example_func.$fslext > & /dev/null
> mri_info --o /tmp/reg-feat2anat.rasgood.36869 --ras_good
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$` ;
> set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$`
> cat /tmp/reg-feat2anat.rasgood.36869
> endif
> endif
> echo "example_func ras_good_flag $exf_ras_good" | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> echo example_func ras_good_flag 1
> example_func ras_good_flag 1
> if ( $exf_ras_good ) then
> if ( 1 ) then
> echo "-------------------------------------------------------" | tee
> -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> echo -------------------------------------------------------
> -------------------------------------------------------
> echo "Initializing exf2anat with header" | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> echo Initializing exf2anat with header
> Initializing exf2anat with header
> set cmd = ( $TKR --targ $refvolcor --mov $FeatDir/example_func.$fslext
> --reg $anat2exf_regdat.init --fslregout $exf2anat_init_fslmat
> --regheader )
> set cmd = ( tkregister2_cmdl_cmdl --targ
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> --mov
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> --reg
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init
> --fslregout
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat
> --regheader )
> if ( ! $debug ) set cmd = ( $cmd --noedit )
> if ( ! 1 ) set cmd = ( tkregister2_cmdl_cmdl --targ
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> --mov
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> --reg
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init
> --fslregout
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat
> --regheader --noedit )
> echo $cmd | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> echo tkregister2_cmdl_cmdl --targ
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> --mov
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> --reg
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init
> --fslregout
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat
> --regheader
> tkregister2_cmdl_cmdl --targ
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> --mov
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> --reg
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init
> --fslregout
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat
> --regheader
> $cmd | tee -a $LF
> tee -a
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/reg-feat2anat.log
> tkregister2_cmdl_cmdl --targ
> /proj/dichterlab/BATA/Analysis/FreeSurfer_7/BA0023_V1/mri/brainmask.mgz
> --mov
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/example_func.nii.gz
> --reg
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/anat2exf.register.dat.init
> --fslregout
> /proj/dichterlab/BATA/Analysis/Hammer/1st_Level_censoring/BA0023/BA0023_V1/run1.feat/reg/freesurfer/exf2anat.init.fsl.mat
> --regheader
> tkregister2_cmdl_cmdl: Command not found.
> if ( $status ) exit 1 ;
> if ( 1 ) exit 1
> exit 1
>
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
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#! /bin/tcsh -f
#
# reg-feat2anat
#
# Registers example func to freesurfer using fsl
#
# Original Author: Doug Greve
#
# Copyright ? 2011 The General Hospital Corporation (Boston, MA) "MGH"
#
# Terms and conditions for use, reproduction, distribution and contribution
# are found in the 'FreeSurfer Software License Agreement' contained
# in the file 'LICENSE' found in the FreeSurfer distribution, and here:
#
#
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense
#
# Reporting: freesurfer@nmr.mgh.harvard.edu
#
#
set VERSION = 'reg-feat2anat @FS_VERSION@';
set FeatDir = ();
set subject = ();
set anatvol = brainmask;
set dof = 6;
set bins = 256;
set maxangle = 90;
set cost = corratio;
set debug = 0;
set cleanup = 1;
set usedev = 0;
set manual = 0;
set manual_use_surf = 1;
set manxfm = func2anat;
set DoBETFunc = 0; # Not with FSL 4.0
set title = ();
set UseSPM = 0;
set DoBBR = 1; # On by default
set INorm = 1;
set fmov = ();
set ReDoStandardReg = 1;
set OverwriteExf2Std = 0;
set PrintHelp = 0;
set cmdargs = ($argv);
if($#argv == 0) goto usage_exit;
set n = `echo $argv | egrep -e --version | wc -l`
if($n != 0) then
echo $VERSION
exit 1;
endif
set n = `echo $argv | egrep -e --help | wc -l`
if($n != 0) then
set PrintHelp = 1;
goto usage_exit;
exit 1;
endif
source $FREESURFER_HOME/sources.csh
# Parse the command-line arguments
goto parse_args;
parse_args_return:
# Check the command-line arguments
goto check_params;
check_params_return:
if($?DEV == 0) set DEV = "";
set TKR = tkregister2_cmdl
if($usedev) set TKR = $DEV/$TKR/$TKR
if(! $manual) set TKR = $TKR
set MM = mri_matrix_multiply
if($usedev) set MM = $DEV/$MM/$MM
echo FeatDir is $FeatDir
mkdir -p $FeatDir/reg/freesurfer/tmp
set exf2std_fslmat = $FeatDir/reg/example_func2standard.mat
if(! -e $exf2std_fslmat) then
echo "ERROR: cannot find $exf2std_fslmat. You must register to standard space first."
exit 1;
endif
# Automatically detect the file format
set exfbase = $FeatDir/example_func
if(-e $exfbase.nii.gz) then
setenv FSLOUTPUTTYPE NIFTI_GZ
set fslext = nii.gz;
endif
if(-e $exfbase.nii) then
setenv FSLOUTPUTTYPE NIFTI
set fslext = nii;
endif
if(-e $exfbase.img) then
setenv FSLOUTPUTTYPE ANALYZE
set fslext = img;
endif
if($#fslext == 0) then
echo "ERROR: cannot determine type of fsl output from $exfbase"
exit 1;
endif
set tempvol = $FeatDir/example_func.$fslext
echo "template volume is $tempvol"
set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat
set anat2std_regdat = $FeatDir/reg/freesurfer/anat2std.register.dat
set std2anat_fslmat = $FeatDir/reg/freesurfer/std2anat.fsl.mat
set exf2anat_init_fslmat = $FeatDir/reg/freesurfer/exf2anat.init.fsl.mat
set exf2anat_fslmat = $FeatDir/reg/freesurfer/exf2anat.fsl.mat
set std2exf_regdat = $FeatDir/reg/freesurfer/std2exf.register.dat
set exf2std_regdat = $FeatDir/reg/freesurfer/exf2std.register.dat
set segregdat = $FeatDir/reg/freesurfer/reg.bbr.dat
set stdbrain = $FeatDir/reg/standard.$fslext
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
if(! -e $refvolcor) then
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol
if(! -e $refvolcor/COR-.info) then
echo "ERROR: cannot find $anatvol for $subject "
exit 1;
endif
endif
# Manually check functional-to-anatomical registration
if($manual && $manxfm == func2anat) then
if(! -e $anat2exf_regdat) then
echo "ERROR: you must run without --manual or --manxfm to create registration first"
exit 1;
endif
set cmd = ($TKR --s $subject --mov $tempvol --volview mov\
--reg $anat2exf_regdat --tag)
if($#fmov) set cmd = ($cmd --fmov $fmov)
if($manual_use_surf) set cmd = ($cmd --surf orig);
if($#title) set cmd = ($cmd --title $title);
if(! -e $SUBJECTS_DIR/$subject/mri/orig/COR-001) set cmd = ($cmd --mgz)
echo $cmd
$cmd
if($status) exit 1;
exit 0;
endif
# Manually check standard-to-anatomical registration
if($manual && $manxfm == std2anat) then
if(! -e $anat2std_regdat) then
echo "ERROR: you must run without --manual or --manxfm to create registration first"
exit 1;
endif
set cmd = ($TKR --tag --s $subject --inorm\
--targ $refvolcor --mov $stdbrain --volview mov\
--reg $anat2std_regdat --fslreg $std2anat_fslmat)
if($manual_use_surf) set cmd = ($cmd --surf orig);
if($#title) set cmd = ($cmd --title $title);
echo $cmd
$cmd
if($status) exit 1;
exit 0;
endif
# Manually check function-to-standard registration
if($manual && $manxfm == func2std) then
if(! -e $exf2std_regdat) then
echo "ERROR: you must run without --manual or --manxfm to create registration first"
exit 1;
endif
set cmd = ($TKR --targ $stdbrain \
--mov $FeatDir/example_func.$fslext --volview mov\
--reg $exf2std_regdat --s $subject --tag --inorm);
if($#title) set cmd = ($cmd --title $title);
echo $cmd
$cmd
if($status) exit 1;
exit 0;
endif
# Set up a log file
set LF = $FeatDir/reg/freesurfer/reg-feat2anat.log
if(-e $LF) mv $LF $LF.bak
echo log file is $LF
date | tee -a $LF
pwd | tee -a $LF
echo $0 | tee -a $LF
echo $cmdargs | tee -a $LF
uname -a | tee -a $LF
# Make sure the anatomical is there
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol.mgz
if(! -e $refvolcor) then
set refvolcor = $SUBJECTS_DIR/$subject/mri/$anatvol
if(! -e $refvolcor/COR-.info) then
echo "ERROR: cannot find $anatvol for $subject "
exit 1;
endif
endif
# Create the init exf2anat matrix -- this is not accurate, Just
# gets things lined up. We'll compute a better one below. If
# the input has a valid vox2ras, then use that, otherwise,
# use the std2anat.
if($fslext == img) then
# Cannot trust rasgood with analyze
if( -e $FeatDir/example_func.mat) then
set exf_ras_good = 1;
else
set exf_ras_good = 0;
endif
else
mri_info --o /tmp/reg-feat2anat.rasgood.$$ \
--ras_good $FeatDir/example_func.$fslext >& /dev/null
set exf_ras_good = `cat /tmp/reg-feat2anat.rasgood.$$`;
endif
echo "example_func ras_good_flag $exf_ras_good"| tee -a $LF
if($exf_ras_good) then
echo "-------------------------------------------------------" | tee -a $LF
echo "Initializing exf2anat with header" | tee -a $LF
set cmd = ($TKR \
--targ $refvolcor \
--mov $FeatDir/example_func.$fslext\
--reg $anat2exf_regdat.init \
--fslregout $exf2anat_init_fslmat \
--regheader)
if(! $debug) set cmd = ($cmd --noedit)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
else
echo "-------------------------------------------------------" | tee -a $LF
echo "Initializing exf2anat from crude std2anat" | tee -a $LF
# vox2ras is not valid in exf, so init from crude std2anat
set cmd = ($TKR \
--targ $refvolcor \
--mov $stdbrain \
--reg $anat2std_regdat \
--fslregout $std2anat_fslmat \
--regheader)
if(! $debug) set cmd = ($cmd --noedit)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
cp $std2anat_fslmat $std2anat_fslmat.init
# Compute initial matrix. Binarize because otherwise there
# might be a stretch (due to 12 dof reg to standard), which
# would not be appropriate for a 6 dof reg (I think).
set cmd = ($MM -fsl -bin \
-iim $exf2std_fslmat -iim $std2anat_fslmat \
-om $exf2anat_init_fslmat)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
endif
set outvol = $FeatDir/reg/freesurfer/tmp/exf-in-anat
if(! $UseSPM) then
# Now run the fslregister cmd
set cmd = (fslregister --s $subject --reg $anat2exf_regdat \
--mov $tempvol --dof $dof --bins $bins --cost $cost \
--fslmat $exf2anat_fslmat --fsvol $anatvol.mgz \
--maxangle $maxangle --initfslmat $exf2anat_init_fslmat \
--tmp $FeatDir/reg/freesurfer/tmp --out $outvol.$fslext)
if($DoBETFunc) set cmd = ($cmd --betfunc) # Not with FSL 4.0
echo "" | tee -a $LF
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
if($DoBBR) then
cp $anat2exf_regdat $anat2exf_regdat.bbr.init
set cmd = (bbregister --mov $tempvol --bold --$dof\
--init-reg $anat2exf_regdat --reg $anat2exf_regdat)
echo "" | tee -a $LF
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
endif
else
# Or use SPM2 or SPM5 (but don't tell Steve)
# This will probably only work on x32 machines
set cmd = (spmregister --s $subject --reg $anat2exf_regdat \
--mov $tempvol --fsvol $anatvol \
--tmp $FeatDir/reg/freesurfer/tmp )
echo "" | tee -a $LF
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
if($DoBBR) then
cp $anat2exf_regdat $anat2exf_regdat.bbr.init
set cmd = (bbregister --mov $tempvol --bold --$dof\
--init-reg $anat2exf_regdat --reg $anat2exf_regdat)
echo "" | tee -a $LF
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
endif
# Now create the fsl matrix
set cmd = ($TKR --reg $anat2exf_regdat --mov $tempvol\
--fslregout $FeatDir/reg/freesurfer/exf2anat.fsl.mat \
--noedit)
echo $cmd
$cmd | tee -a $LF
if($status) exit 1;
endif
cp $anat2exf_regdat $FeatDir/reg/freesurfer/register.dat
if($ReDoStandardReg) then
# Create tkr anat2std registration
set tmp = $SUBJECTS_DIR/$subject/mri/transforms/reg.mni152.2mm.dat
if(-e $tmp) then
set cmd = (cp $tmp $anat2std_regdat)
else
set cmd = (fslregister --mov $stdbrain --s $subject --reg $anat2std_regdat --dof 12)
endif
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Create tkr exf2std registration
set cmd = (mri_matrix_multiply -im $anat2exf_regdat -iim $anat2std_regdat -om $exf2std_regdat)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Create fsl exf2std registration
set cmd = ($TKR --targ $stdbrain --mov $FeatDir/example_func.$fslext \
--reg $exf2std_regdat --fslregout $FeatDir/reg/freesurfer/example_func2standard.mat)
if(! $debug) set cmd = ($cmd --noedit)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Overwrite the feat-created fsl exf2std?
if($OverwriteExf2Std) then
cp $FeatDir/reg/example_func2standard.mat $FeatDir/reg/example_func2standard.mat.bak
cp $FeatDir/reg/freesurfer/example_func2standard.mat $FeatDir/reg/example_func2standard.mat
endif
# Create tkr std2exf registration
set cmd = (mri_matrix_multiply -im $anat2std_regdat -iim $anat2exf_regdat -om $std2exf_regdat)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
else
# Create a tkr matrix to map exf2std
set cmd = ($TKR --targ $stdbrain \
--mov $FeatDir/example_func.$fslext \
--fslreg $FeatDir/reg/example_func2standard.mat \
--reg $std2exf_regdat --noedit)
echo "" | tee -a $LF
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
# Compute fsl std2anat
set cmd = ($MM -fsl \
-im $FeatDir/reg/freesurfer/exf2anat.fsl.mat \
-iim $FeatDir/reg/example_func2standard.mat \
-om $FeatDir/reg/freesurfer/std2anat.fsl.mat)
echo "" | tee -a $LF
echo $cmd | tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
endif
# Now compute fsl.mat anat2std
echo "-------------------------------------------------------" | tee -a $LF
set cmd = ($TKR --s $subject --targ $refvolcor --mov $stdbrain \
--reg $anat2std_regdat --fslregout $std2anat_fslmat)
if(! $debug) set cmd = ($cmd --noedit)
echo $cmd | tee -a $LF
$cmd | tee -a $LF
if($status) exit 1;
# Create cmd to check
set cmd = ($TKR --s $subject --mov $tempvol)
set cmd = ($cmd --reg $anat2exf_regdat)
set cmd = ($cmd --fslreg $exf2anat_fslmat)
set cmd = ($cmd --surf orig); # for visual inspection
echo ""
echo "To visually check your results, run:" | tee -a $LF
echo $cmd --tag | sed 's/_cmdl//g' | tee -a $LF
# note: the sed will remove the _cmdl from the tkregister2 cmd
echo ""
echo ""
if($cleanup == 0) then
# Create an identity matrix for the output
set outvolreg = $outvol.fsreg.dat
rm -f $outvolreg
echo $subject >> $outvolreg
echo 0 >> $outvolreg
echo 0 >> $outvolreg
echo .1 >> $outvolreg
echo "1 0 0 0" >> $outvolreg
echo "0 1 0 0" >> $outvolreg
echo "0 0 1 0" >> $outvolreg
echo "0 0 0 1" >> $outvolreg
echo "Or you can run:" | tee -a $LF
set tkregcheckcmd2 = (tkregister2_cmdl --s $subject --mov $outvol)
set tkregcheckcmd2 = ($tkregcheckcmd2 --reg $outvolreg --surf orig);
echo $tkregcheckcmd2 | tee -a $LF
echo ""
else
rm -fr $FeatDir/reg/freesurfer/tmp
endif
date | tee -a $LF
echo "reg-feat2anat done" | tee -a $LF
exit 0;
###############################################
############--------------##################
parse_args:
set cmdline = ($argv);
while( $#argv != 0 )
set flag = $argv[1]; shift;
switch($flag)
case "--feat":
case "--featdir":
if ( $#argv == 0) goto arg1err;
set FeatDir = $argv[1]; shift;
breaksw
case "--s":
case "--subject":
if ( $#argv == 0) goto arg1err;
set subject = $argv[1]; shift;
breaksw
case "--dof":
if ( $#argv == 0) goto arg1err;
set dof = $argv[1]; shift;
breaksw
case "--bins":
if ( $#argv == 0) goto arg1err;
set bins = $argv[1]; shift;
breaksw
case "--cost":
if ( $#argv == 0) goto arg1err;
set cost = $argv[1]; shift;
breaksw
case "--maxangle":
if ( $#argv == 0) goto arg1err;
set maxangle = $argv[1]; shift;
breaksw
case "--fslmat":
if ( $#argv == 0) goto arg1err;
set fslmat = $argv[1]; shift;
breaksw
case "--fsreg":
if ( $#argv == 0) goto arg1err;
set fsreg = $argv[1]; shift;
breaksw
case "--title":
if( $#argv < 1) goto arg1err;
set title = $argv[1]; shift;
breaksw
case "--no-bet":
set DoBETFunc = 0;
breaksw
case "--bet":
set DoBETFunc = 1;
breaksw
case "--spm":
set UseSPM = 1;
breaksw
case "--bbr":
case "--segreg":
set DoBBR = 1;
breaksw
case "--no-bbr":
set DoBBR = 0;
breaksw
case "--fmov":
if($#argv < 1) goto arg1err;
set fmov = $argv[1]; shift;
breaksw
case "--overwrite-exf2std":
set OverwriteExf2Std = 1;
breaksw
case "--inorm":
set Inorm = 1;
breaksw
case "--no-inorm":
set Inorm = 0;
breaksw
case "--debug":
set verbose = 1;
set echo = 1; # turns on terminal echoing
set debug = 1;
breaksw
case "--nocleanup":
set cleanup = 0;
breaksw
case "--manual":
set manual = 1;
breaksw
case "--manxfm":
if ( $#argv == 0) goto arg1err;
set manxfm = $argv[1]; shift;
set manual = 1;
breaksw
case "--manual-no-surf":
set manual_use_surf = 0;
breaksw
case "--usedev":
set usedev = 1;
breaksw
default:
echo "ERROR: flag $flag not recognized"
exit 1;
breaksw
endsw
end
goto parse_args_return;
############--------------##################
############--------------##################
check_params:
if($DoBBR) then
which bbregister > /dev/null
if($status) then
echo ""
echo "ERROR: reg-feat2anat is currently configured to run bbregister."
echo "However, it cannot be found in your path. Make sure it is"
echo "in your path and then rerun reg-feat2anat. Alternatively, you"
echo "can run reg-feat2anat with --no-bbr, but the results might not"
echo "be as accurate"
echo ""
exit 1;
endif
endif
if($#FeatDir == 0) then
echo "ERROR: must specify feat dir"
exit 1;
endif
if(! -e $FeatDir) then
echo "ERROR: cannot find feat dir $FeatDir"
exit 1;
endif
if(! $manual) then
if($#subject == 0) then
echo "ERROR: must specify a FreeSurfer subject"
exit 1;
endif
else
set anat2exf_regdat = $FeatDir/reg/freesurfer/anat2exf.register.dat
if(! -e $anat2exf_regdat) then
echo "ERROR: cannot find $anat2exf_regdat"
exit 1;
endif
#set subject = `cat $anat2exf_regdat | head -1`;
set subject = `reg2subject --r $anat2exf_regdat`;
endif
if($?SUBJECTS_DIR == 0) then
echo "ERROR: FreeSurfer environment variable SUBJECTS_DIR not defined"
exit 1;
endif
if(! -e $SUBJECTS_DIR) then
echo "ERROR: FreeSurfer SUBJECTS_DIR $SUBJECTS_DIR not found"
exit 1;
endif
if(! -e $SUBJECTS_DIR/$subject) then
echo "ERROR: cannot find FreeSurfer subject $subject in $SUBJECTS_DIR"
exit 1;
endif
if($manxfm != "func2anat" && $manxfm != "std2anat" && $manxfm != "func2std") then
echo "ERROR: manxfm is $manxfm, must be func2anat, std2anat, func2std"
exit 1;
endif
goto check_params_return;
############--------------##################
############--------------##################
arg1err:
echo "ERROR: flag $flag requires one argument"
exit 1
############--------------##################
############--------------##################
usage_exit:
echo ""
echo "USAGE: reg-feat2anat"
echo ""
echo " --feat dir : directory in which to find example_func"
echo " --subject id : FreeSurfer subjectid"
echo ""
echo "Optional flags and arguments:"
echo ""
echo " --overwrite-exf2std : replace Feat-generated example_func2standard"
echo ""
echo " --manual : interactively view/edit registration"
echo " --manxfm xfmtype : interactively view/edit registration for xfmtype"
echo " xfmtype can be: func2anat, std2anat, or func2std"
echo " --dof dof : FLIRT DOF (default is $dof)"
echo " --bins bins : FLIRT bins (default is $bins)"
echo " --cost cost : FLIRT cost (default is $cost)"
echo " --maxangle angle : FLIRT max search angle (default is $maxangle)"
echo " --bet : run betfunc on example_func (not with FSL 4.0)"
echo " "
echo " --title : title for tkregister window"
echo " --no-bbr : do not use boundary-based registration"
echo " --spm : use SPM instead of flirt, 6 dof only"
echo " --no-inorm : do not inorm when running tkregister2"
echo " --fmov fmov : for tkregister2"
echo " --version : print version and exit"
echo " --help : print help and exit"
echo " --debug : turn on debugging"
echo ""
if(! $PrintHelp) exit 1;
echo $VERSION
cat $0 | awk 'BEGIN{prt=0}{if(prt) print $0; if($1 == "BEGINHELP") prt = 1 }'
exit 1;
#---- Everything below here is printed out as part of help -----#
BEGINHELP
Registers FSL-Feat example_func (exf) to FreeSurfer anatomical (anat).
If the geometry in the header for the example_func is "good", then
creates an initial matrix between the anat and the exf based on
headers of the two volumes. NIFTI should always have a good
geometry. ANALYZE can have a good geometry if a valid SPM-style .mat
file exits (ie, example_func.mat). If the geometry is good, this
should work regardless of whether the exf is in radiological
convention (ie, negative determinant) or neurological convention (ie,
positive determinant).
If the example_func geometry is not good, then it uses the
registration between the example_func and standard space is used to
generate an approximate initial registration between the example_func
and the anat -- this just assures that the two are in the same
orientation at the start. The registration matrices for FSL and FS
have different interpretations and formats.
Creates featdir/reg/freesurfer with the following files:
anat2std.register.dat - init FS reg from anat to FSL-standard.
std2anat.fsl.mat - init FSL reg from FSL-standard to anat.
exf2anat.init.fsl.mat - init FSL reg from example_func to anat.
exf2anat.fsl.mat - final FSL reg from example_func to anat.
anat2exf.register.dat - final FS reg from example_func to anat.
register.dat - same as anat2exf.register.dat
example_func2standard.mat - can be used to replace feat-generated
anat2exf.register.dat is the final product of this script and is what is
used by other FreeSurfer programs.
After subject data has been resampled to standard space, you can still
interface with freesurfer using std2anat.fsl.mat instead of
anat2exf.register.dat.
Creates log file: reg/freesurfer/reg-feat2anat.log
REQUIRED ARGUMENTS
--feat dir
Path to Feat directory.
--subject id
FreeSurfer subject identifier as found in SUBJECTS_DIR.
OPTIONAL FLIRT ARGUMENTS
These arguments are passed to flirt
--dof dof
--bins bins
--cost cost
--maxangle angle : passed as max_angle for -searchrx, -searchry, and -searchrz
--overwrite-exf2std
Overwrite feat-generated example_func2standard.mat with one generated by
reg-feat2anat. This one is generated by concatenating the example_func2anat
and anat2standard transforms. This is recommended when the high-level
analyses will be done in surface-space.
OTHER ARGUMENTS
--manual
Interactively view or edit registration with tkregister2. You must have
already run reg-feat2anat without --manual to create the initial registration.
Equivalent to --manxfm func2anat.
--manxfm xfmtype
xfmtype can be func2anat, std2anat, or func2std. Implies --manual.
Interactively view or edit registration with tkregister2. You must have
already run reg-feat2anat without --manxfm to create the initial registration.
--version : print version and exit
--help : print help and exit
--debug : turn on debugging
EXAMPLE
# Assume a data set exists called fbert.$fslext, where fslext is either
# img, nii, or nii.gz. It determines the file format based on the format
# of the example_func. FSLOUTPUTTYPE is then set accordingly.
#
# Analyze fbert.$fslext with Feat to generate directory fbert.feat
# Register fbert.feat to subject bert:
reg-feat2anat --feat fbert.feat --subject bert --overwrite-exf2std
# View/check the registration
reg-feat2anat --feat fbert.feat --subject bert --manual
# If the registration has catastropically failed, then check that
# the registration to standard space did not fail:
reg-feat2anat --feat fbert.feat --subject bert --manxfm func2std
# Overlay zmap onto the bert's orig volume. Set the threshold at z=1.3
tkmedit bert orig -overlay ./fbert.feat/stats/zstat1.$fslext \
-overlay-reg ./fbert.feat/reg/freesurfer/anat2exf.register.dat \
-fthresh 1.3 -fmid 2.3 -fslope 1
# Overlay zmap onto the standard volume. Set the threshold at z=1.3
tkmedit -f $FSLDIR/etc/standard/avg152T1_brain.$ext \
-overlay ./fbert.feat/stats/zstat1.$fslext \
-overlay-reg ./fbert.feat/reg/freesurfer/std2exf.register.dat \
-fthresh 1.3 -fmid 2.3 -fslope 1
# Resample fbert.feat onto the surface
feat2surf --feat fbert.feat
SEE ALSO
feat2surf, aseg2feat, aparc2feat, tkmedit, tksurfer, mris_preproc,
mri_glmfit, tkregister2, fslregister
------------------------------
Message: 3
Date: Thu, 12 Nov 2020 09:23:13 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Extract he value of area and volume in the
fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}
{Disarmed}
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <da77b4be-7d20-7236-2be3-32d1436f2347@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
No, the area will be under the "Mean" column. Sorry, I know it is
confusing. Also, you will just want to use the 2nd row. You can
eliminate the first row with --exclude 0
On 11/12/2020 5:39 AM, ??? wrote:
>
> ????????External Email - Use Caution
>
> Thank you very much, I get?lh_areapial.avgwf.dat and?lh_areapial.sum
> file after the?mri_segstats command
>
> (1) Does the lh_areapial.avgwf.dat contain areas value for all my subject?
>
> (2) When I extract the volumes, the lh_volume.sum displays the unit
> for the volume is Area_mm2?Blue color). Is this correct?
>
>
> ColHeaders ?Index SegId NVertices Area_mm2 ?StructName ?Mean ? ? ? ?
> ?StdDev ? ? ?Min ? ? ? ?Max ? ? Range
> ? ? ? ? ? ? ? 1 ? 0 ? ?161058 81037.1 ? Seg0000 ? 242940.3281 ?
> ?0.7312 ? ? 0.0000 ? ? 3.8885 3.8885
> ? ? ? ? ? ? ? 2 ? 1 ? ? ?2784 1182.3 ? ?Seg0001 ? ?3760.6619 ? ?
> 0.2525 ? ? 0.7136 1.8140 ? ? 1.1005
>
> Following is the code for extracting volumes
> mri_segstats
> --i qdec/Volume_15_L/y.mgh (y.mgh was created after Qdec)
> --slabel fsaverage lh lh.volume.label (This was the label extracted
> from the fsaverage after multi-correction)
> --avgwf lh_volume.avgwf.dat (output file)
> --accumulate
> --sum lh_volume.sum (output file)
>
>
>
> -----????-----
> *???:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
> *????:*2020-11-11 23:58:20 (???)
> *???:* freesurfer@nmr.mgh.harvard.edu
> *??:*
> *??:* Re: [Freesurfer] Extract he value of area and volume in the
> fsaverage for every subject {Disarmed} {Disarmed} {Disarmed}
>
> Sorry, try this
>
> mri_segstats
> --i qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
> --slabel fsaverage lh lh.areapial.label (This was the label
> extracted from the fsaverage after multi-correction)
> --avgwf lh_areapial.avgwf.dat (output file)
> --accumulate
> --sum lh_areapial.sum (output file)
> On 11/5/2020 10:26 PM, ??? wrote:
>>
>> ????????External Email - Use Caution
>>
>> I tried following codes according to the suggestions, the
>> terminal reported an error: cannot do frame average without input
>> volume
>>> mri_segstats
>>> --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
>>> --slabel fsaverage lh lh.areapial.label (This was the label
>>> extracted from the fsaverage after multi-correction)
>>> --avgwf lh_areapial.avgwf.dat (output file)
>>> --accumulate
>>> --sum lh_areapial.sum (output file)
>>>
>>>
>>>
>> -----????-----
>> *???:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
>> *????:*2020-11-05 22:37:07 (???)
>> *???:* freesurfer@nmr.mgh.harvard.edu
>> *??:*
>> *??:* Re: [Freesurfer] Extract he value of area and volume in
>> the fsaverage for every subject {Disarmed} {Disarmed}
>>
>> Try
>> --slabel fsaverage lh /path/to/lh.areapial.label
>>
>> On 11/2/2020 10:24 PM, ??? wrote:
>>>
>>> ????????External Email - Use Caution
>>>
>>> Thank you very much! I tried to extract the areas with the
>>> following codes:
>>> mri_segstats
>>> --seg qdec/Areapial_15_L/y.mgh (y.mgh was created after Qdec)
>>> --slabel lh.areapial.label (This was the label extracted
>>> from the fsaverage after multi-correction)
>>> --avgwf lh_areapial.avgwf.dat (output file)
>>> --accumulate
>>> --sum lh_areapial.sum (output file)
>>> I did not get a text file including the areas of all
>>> subjects. Is this code correct?
>>>
>>> -----????-----
>>> *???:*"Douglas N. Greve" <dgreve@mgh.harvard.edu>
>>> *????:*2020-11-02 23:36:14 (???)
>>> *???:* freesurfer@nmr.mgh.harvard.edu
>>> *??:*
>>> *??:* Re: [Freesurfer] Extract he value of area and
>>> volume in the fsaverage for every subject {Disarmed}
>>>
>>> I think the reason for this may be that the data in
>>> fsaverage space (after mris_preproc) will have had a
>>> jacobian correction which will not be in data on the
>>> native surface. For this reason, I would not use #1. #2
>>> is fine.You can apply your label in fsaverage space to
>>> the y.mgh used as input to mri_segstats specifying the
>>> label using --slabel and using --avgwf output and also
>>> use --accumulate; run it with --help for more info. This
>>> will create a text file of the areas or volumes
>>> (depending upon which y.mgh you input) all your subjects
>>> for that label.
>>>
>>>
>>> On 10/30/2020 10:37 PM, ??? wrote:
>>>>
>>>> ????????External Email - Use Caution
>>>>
>>>> Dear Professors:
>>>> ? I compared the thickness, area, volume in the mild
>>>> traumatic brain injury patients with health control by
>>>> FreeSurFer, and found statistic difference region in
>>>> the cortex area, volume?respectively. I defined
>>>> the?statistic difference regions as a label on the
>>>> fsaverage and mapped this label to subjects by
>>>> Qdec/mri_label2label. The label defined on the
>>>> fsaverage was mapped onto all subjects successfully,
>>>> and the label in subjects matched well with the
>>>> inflated cortex of subjects in?Freeview? Then the value
>>>> of the label in every single subjects was extracted,
>>>> and I found that there is no statistic difference in
>>>> the value regarding to the area and volume?between the
>>>> mild traumatic brain injury patients and health control
>>>> subjects. Following are my questions:
>>>>
>>>> (1)Can I carry out correlation analysis between
>>>> the?cortex area and volume with the behavior scores
>>>> through these non-statistical extracted values?
>>>> (2)Can I?extract the value of?cortex area and volume in
>>>> the standard space for every TBI and health control
>>>> subjects, and carry out correlation analysis between
>>>> the?cortex area and volume with the behavior scores.
>>>> How can I extract the value of?cortex area and volume
>>>> in the standard space for every TBI and health control
>>>> subjects
>>>>
>>>> Best wishes
>>>> Mengjun Li
>>>>
>>>>
>>>> -----????-----
>>>> *???:*"Douglas N. Greve" <dgreve@MGH.HARVARD.EDU>
>>>> *????:*2020-10-30 23:40:30 (???)
>>>> *???:* freesurfer@nmr.mgh.harvard.edu
>>>> *??:*
>>>> *??:* Re: [Freesurfer] Extract he value of area and
>>>> volume in the fsaverage for every subject
>>>>
>>>> Do you mean you compared your TBI subjects against
>>>> fsaverage? That is not proper methodology.
>>>>
>>>> On 10/29/2020 9:51 PM, ??? wrote:
>>>>>
>>>>> ????????External Email - Use Caution
>>>>>
>>>>>> Dear FreeSurfer Developers:
>>>>>>
>>>>>> ? ?I compared the cortical thickness, area,
>>>>>> volume in the mild traumatic brain injury
>>>>>> patients with health control by FreeSurFer, and
>>>>>> found a?statistic difference region in the cortex
>>>>>> area and volume after correction. How can I
>>>>>> extract the value of cortex area and volume for
>>>>>> every subject in the fsaverage with the?code
>>>>>> of?mri_segstats
>>>>>>
>>>>>> FreeSurfer
>>>>>> version:?freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
>>>>>> Platform: macOS High Sierra.
>>>>>>
>>>>>> Best wishes
>>>>>> Mengjun Li
>>>>>> Second Xiangya Hospital
>>>>>> Central South University
>>>>>
>>>>> _______________________________________________
>>>>> Freesurfer mailing list
>>>>> Freesurfer@nmr.mgh.harvard.edu
>>>>> *MailScanner has detected a possible fraud attempt
>>>>> from "secure-web.cisco.com" claiming to be*
>>>>>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>>
>>>>
>>>> _______________________________________________
>>>> Freesurfer mailing list
>>>> Freesurfer@nmr.mgh.harvard.edu
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>>>> "secure-web.cisco.com" claiming to be*
>>>>
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>>
>>>
>>> _______________________________________________
>>> Freesurfer mailing list
>>> Freesurfer@nmr.mgh.harvard.edu
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>>> "secure-web.cisco.com" claiming to be*
>>>
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>>
>>
>> _______________________________________________
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
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>> "secure-web.cisco.com" claiming to be*
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>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
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------------------------------
Message: 4
Date: Thu, 12 Nov 2020 09:24:44 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Sulc maps
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <cd77ece0-35ab-1f1e-8700-6218a34303d4@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
I think it is probably just scaling, but it has been a long time since
5.3 and 6.0
On 11/9/2020 10:10 AM, Reza Rajimehr wrote:
>
> ????????External Email - Use Caution
>
> Hi,
>
> In the .sulc files, the range of sulcal depth values are very
> different (about 10 times higher) in Freesurfer v6 compared to
> Freesurfer v5.3. Is there just a simple scaling factor here, or the
> procedure for calculating sulcal depth has been changed?
>
> Thanks,
> Reza
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
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------------------------------
Message: 5
Date: Thu, 12 Nov 2020 09:26:58 -0500
From: "Douglas N. Greve" <dgreve@mgh.harvard.edu>
Subject: Re: [Freesurfer] Help with MRI labels
To: <freesurfer@nmr.mgh.harvard.edu>
Message-ID: <59e98840-3eb6-7ccd-c866-dabd9230def1@mgh.harvard.edu>
Content-Type: text/plain; charset="utf-8"
So you want the AAL atlas on the surface? If so, then run recon-all on
the AAL anatomical T1w volume template, then use mri_vol2surf to sample
the labels on the surface, then use this surface segmentation or extract
labels (mri_cor2label with --surf option) or convert to an annotation
(mris_seg2annot)
On 11/11/2020 11:32 AM, Alberto Del Cerro Leon wrote:
>
> ????????External Email - Use Caution
>
> Good afternoon, my name is Alberto del Cerro and I am a PhD student in
> the cognitive and computational neuroscience laboratory (LNCyC) at the
> biomedical technology center (CTB) of the Polytechnic University of
> Madrid (UPM). I am currently extracting the structural data from the
> T1 images of my project and I would like to extract the volume,
> thickness and curvature data in the regions of interest where I
> obtained results in electrophysiology (MEG). The point is that for
> this data I used the AAL atlas and I would like to use these regions
> to obtain structural data in FreeSurfer. Researching on the internet I
> have read that this is possible with the mri_label2vol command but I
> would like to know how I can proceed to obtain this data. Can you
> guide me in this process?
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
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------------------------------
Message: 6
Date: Thu, 12 Nov 2020 14:52:51 +0000
From: "Nasr, Shahin,Ph.D." <shahin.nasr@mgh.harvard.edu>
Subject: [Freesurfer] mris_pmake error - freadFloat: fread failed
To: "Freesurfer@nmr.mgh.harvard.edu" <Freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<MN2PR04MB639940501B3C7106BD92CEF9A3E70@MN2PR04MB6399.namprd04.prod.outlook.com>
Content-Type: text/plain; charset="iso-8859-1"
Hi Surfers,
For one subject, when I run mris_pmake as below:
mris_pmake --subject <Subject_Name> --hemi lh --surface smoothwm --mpmProg pathFind --mpmArgs vertexStart:<Start Vertex>,vertexEnd:<End Vertex> --mpmOverlay euclidean
I get the following error:
mris_pmake error - freadFloat: fread failed
This error appears irrespective of the Start/End vertex, as far as I see. I guess this error is because a file in the subject's brain recon is corrupted. But unfortunately, the error message is not helpful. I even tried to open the error.log. But I do not
see any further info there.
Any suggestions?
Shahin
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Message: 7
Date: Thu, 12 Nov 2020 14:56:44 +0000
From: "Park, James" <james.kunwoo.park@emory.edu>
Subject: [Freesurfer] Support: Password Request for Ubuntu_710 to
download Freesurfer on Windows 10 {Disarmed}
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<BN6PR05MB347448A4D42AC4A744E66EBFB3E70@BN6PR05MB3474.namprd05.prod.outlook.com>
Content-Type: text/plain; charset="windows-1252"
External Email - Use Caution
Dear Freesurfer Team,
Hello, my name is James Park and I have recently been trying to utilize Freesurfer on a new Windows Computer.
I was able follow the instructions provided on :
https://secure-web.cisco.com/1eXouftPDgg37AuJADlljMENUWBEUfGROCh_5ifJ-wvqNhQPRfgpHWXJB0SkxVJsoLoBoMaMOW-JIUWuRvlPsLVfRR3D6vJxKSTB8me_P6MfSy2wa7QdKRD2dN9wYwmNcJpQTyK1pIc_jm6pe-D_nM6G7LkSa6DBhjpVTULK58OVW-zUor9RC6G3dqGxU6s-Nxk2sA8fnPhcfAWRhcvbOSZ-IQIK8Jff_nU_YgrA5zgv5jf4bBhCUaaBDb4JpSxHeO0IHaPdBbKIiLNGae1DnTA/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FVM_67_win<https://secure-web.cisco.com/1EEXroSruFwS_tEl0TiiJP0980pQWotjNew0Aa2WayNcN9XIAsa_lnpX81A18p2TZlVeS3NRopFpcDt-6vP5MHdhCQP2WlE-PHx-9uBYSFVFHrOcxjnwmcLvL1dFyDPmLZ-ezbXwBJ7qY4Ymwr5WvVsbboadccfHvnsBF7_WLb6nKbll9AqPXf6CjsaDEAGejXnPP4T8tHSpKCffevWtPbmlQR9YFic9tP8CTqbGarNuKLATUwJ4zCd9sTrmbH4OnNg-czGcIRCW9s6mucuJpbg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FVM_67_win>
but unfortunately was unable to log into the desktop of the virtual machine because it requires a password for the ?developer? account.
I noticed in previous mailing archives this password was sent privately ? could I also receive this password by chance?
Thank you for your help in advance.
Sincerely,
James Park
email: james.kunwoo.park@emory.edu<mailto:james.kunwoo.park@emory.edu>
________________________________
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If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).
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Message: 8
Date: Thu, 12 Nov 2020 16:11:05 +0100
From: fsbuild <fsbuild@contbay.com>
Subject: Re: [Freesurfer] Support: Password Request for Ubuntu_710 to
download Freesurfer on Windows 10 {Disarmed} {Disarmed}
To: freesurfer@nmr.mgh.harvard.edu
Cc: james.kunwoo.park@emory.edu
Message-ID: <1605193865.5fad5089d41d1@trashmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
Hello James,
I will send the password directly to your email shortly..
-R.
On Nov 12, 2020, at 09:56, Park, James <james.kunwoo.park@emory.edu> wrote: External Email - Use Caution Dear Freesurfer Team, Hello, my name is James Park
and I have recently been trying to utilize Freesurfer on a new Windows Computer. I was able follow the instructions provided on : MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/14p-Zxk74tVoTu8QrA0S0_iUpBL5mkrv-GBxx2q6_vSnVies3A0Nlh8V4Gw5KMhTvGClsEJSe8E08kwA_89IbVRFHrHR8E9A_ZkMNa0gCRdHB73R6ydUAX7TdEfGKlGrf_Ejyv_ofweBWPwuXwsxDveTZDH7cnt0zVC_kSeB0B2XQuOeryp5GrPAKfXuJkKsoDKzqpX_vEReN_N53FA7DVMollzKnmN-yWu97RvTstR1ggpECGAPX3WuxzWO-3grxMx6IrlVUhsQP26NSnwN0dQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2F%2FVM_67_win%C2%A0but
unfortunately was unable to log into the desktop of the virtual machine because it requires a password for the ?deve
loper? account. I noticed in previous mailing archives this password was sent privately ? could I also receive this password by chance? Thank you for your help in advance. Sincerely,James Parkemail: james.kunwoo.park@emory.edu This
e-mail message (including any attachments) is for the sole use ofthe intended recipient(s) and may contain confidential and privilegedinformation. If the reader of this message is not the intendedrecipient, you are hereby notified that any dissemination, distributionor
copying of this message (including any attachments) is strictlyprohibited.If you have received this message in error, please contactthe sender by reply e-mail message and destroy all copies of theoriginal message (including attachments)._______________________________________________Freesurfer
mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Message: 9
Date: Thu, 12 Nov 2020 16:17:20 +0100
From: Alberto Del Cerro Leon <bertocerron@gmail.com>
Subject: Re: [Freesurfer] Help with MRI labels {Disarmed}
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Message-ID:
<CAKXUO45m+EXZDeCpi_7he6jcTaMWoLLGYQ4gpSVCEcFyYnekmA@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
External Email - Use Caution
I want to obtain gray matter, withe matter volume, thickness and curvature
based on AAL segmentation.
El jue., 12 nov. 2020 15:27, Douglas N. Greve <dgreve@mgh.harvard.edu>
escribi?:
> So you want the AAL atlas on the surface? If so, then run recon-all on the
> AAL anatomical T1w volume template, then use mri_vol2surf to sample the
> labels on the surface, then use this surface segmentation or extract labels
> (mri_cor2label with --surf option) or convert to an annotation
> (mris_seg2annot)
>
>
> On 11/11/2020 11:32 AM, Alberto Del Cerro Leon wrote:
>
> External Email - Use Caution
> Good afternoon, my name is Alberto del Cerro and I am a PhD student in the
> cognitive and computational neuroscience laboratory (LNCyC) at the
> biomedical technology center (CTB) of the Polytechnic University of Madrid
> (UPM). I am currently extracting the structural data from the T1 images of
> my project and I would like to extract the volume, thickness and curvature
> data in the regions of interest where I obtained results in
> electrophysiology (MEG). The point is that for this data I used the AAL
> atlas and I would like to use these regions to obtain structural data in
> FreeSurfer. Researching on the internet I have read that this is possible
> with the mri_label2vol command but I would like to know how I can proceed
> to obtain this data. Can you guide me in this process?
>
> _______________________________________________
> Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
>
https://secure-web.cisco.com/1Anx-jqyTFx_zp_nRElN9YnBQYNKuxs-SalxSsOz_ANH05UryTFARX6Jt6pBxjWvamuz7NMWZHlvZ4pxrzGVnGWkmzVYQlK0BsYZD_AyQfdqwrwohLYliOxLyTrtTSuqOM863QBKVnU4oYcMspXiVW9tgZJNlU3ndNsx-UUdG-k5QKP76Ql3MxkJFyFIUIasLjtD-J7SicWx_7SZWz_CFNvG8SbThvs5XsieCHbXOgmwSm1sL5nJIhvM9CVCqabpp6rDIqtHFsa52Yr4xdKfr4g/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
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End of Freesurfer Digest, Vol 201, Issue 19
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