[Freesurfer] Unpacking error
Freesurfer team,
Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and
v5.3.0.
The command line is:
unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
$DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK
And I get the error message:
$Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $
/home/jbang/Projects/replay/log
-src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ
/home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg
/home/jbang/Projects/replay/log//
Wed Feb 3 18:12:41 EST 2016
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug
11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23
nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux
PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC
CompilerVersion: 30400
cpu166.cabiatl.com
Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14
15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
Wed Feb 3 18:12:41 EST 2016
Log File is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log
INFO: Logfile is
/home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is
/home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile
INFO: status file is
/home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status
Scanning directory Wed Feb 3 18:12:41 EST 2016
mri_parse_sdcmdir --sortbyrun --d
/home/jbang/Projects/replay/epi//replay01/DICOM/day1 --o
/home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile
--status /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72
74 76 78 80 82 84 86 88 90 92 94 96 98 100
Done scanning Wed Feb 3 18:17:33 EST 2016
--
2localizer ok 512 512 3 1 2_loc02.dcm
3 fMRI_physio_1_decoder ok 74 74 33 150 1_dec01.dcm
5 fMRI_physio_2_decoder ok 74 74 33 150 1_dec02.dcm
7 fMRI_physio_3_decoder ok 74 74 33 150 1_dec03.dcm
9 fMRI_physio_4_decoder ok 74 74 33 150 1_dec04.dcm
11 fMRI_physio_5_decoder ok 74 74 33 150 1_dec05.dcm
13 fMRI_physio_6_decoder ok 74 74 33 150 1_dec06.dcm
15 fMRI_physio_7_decoder ok 74 74 33 150 1_dec07.dcm
17 fMRI_physio_8_decoder ok 74 74 33 150 1_dec08.dcm
19 fMRI_physio_9_decoder ok 74 74 33 150 1_dec09.dcm
21 fMRI_physio_10_decoder ok 74 74 33 150 1_dec10.dcm
23 fMRI_physio_1_retinotopy ok 74 74 33 120 1_retino01.dcm
25 fMRI_physio_2_retinotopy ok 74 74 32 120 1_retino02.dcm
27 fMRI_physio_3_retinotopy ok 74 74 32 120 1_retino03.dcm
29 fMRI_physio_4_retinotopy ok 74 74 32 120 1_retino04.dcm
31 fMRI_physio_5_retinotopy ok 74 74 32 120 1_retino05.dcm
35 T1_MEMPRAGE ok 256 256 176 4 1_T1_MEMPRAGE_35.dcm
36 T1_MEMPRAGE ok 256 256 176 1 1_RMS.dcm
error reading "file4": illegal operation on a directory
while executing
"gets $FileId line"
(procedure "ReadSeqCfg" line 11)
invoked from within
"ReadSeqCfg $seqcfgfile"
invoked from within
"if { [info exists seqcfgfile] } {
set SeqCfgList [ReadSeqCfg $seqcfgfile];
}"
(file "/home/jbang/freesurfer//bin/unpacksdcmdir.tcl" line 1048)
This same error message appeared on both v4.5.0 and v5.3.0.
Do you have any clue to fix it?
Thank you for your help.
Best,
Ji Won
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[Freesurfer] unpacking error
Dear. Freesurfer team.
Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and
v5.3.0.
The command line is:
unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
$DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK
And I get the error message:
$Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $
/home/jbang/Projects/replay/log
-src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ
/home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg
/home/jbang/Projects/replay/log//
Wed Feb 3 18:12:41 EST 2016
mri_convert -all-info
ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion:
$Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug
11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23
nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux
PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC
CompilerVersion: 30400
cpu166.cabiatl.com
Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14
15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
Wed Feb 3 18:12:41 EST 2016
Log File is /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log
INFO: Logfile is
/home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log
SkipMoCo 0
Scanning source directory ...
INFO: summary file is
/home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile
INFO: status file is
/home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status
Scanning directory Wed Feb 3 18:12:41 EST 2016
mri_parse_sdcmdir --sortbyrun --d
/home/jbang/Projects/replay/epi//replay01/DICOM/day1 --o
/home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile
--status /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status
0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 36
38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 72
74 76 78 80 82 84 86 88 90 92 94 96 98 100
Done scanning Wed Feb 3 18:17:33 EST 2016
--
2localizer ok 512 512 3 1 2_loc02.dcm
3 fMRI_physio_1_decoder ok 74 74 33 150 1_dec01.dcm
5 fMRI_physio_2_decoder ok 74 74 33 150 1_dec02.dcm
7 fMRI_physio_3_decoder ok 74 74 33 150 1_dec03.dcm
9 fMRI_physio_4_decoder ok 74 74 33 150 1_dec04.dcm
11 fMRI_physio_5_decoder ok 74 74 33 150 1_dec05.dcm
13 fMRI_physio_6_decoder ok 74 74 33 150 1_dec06.dcm
15 fMRI_physio_7_decoder ok 74 74 33 150 1_dec07.dcm
17 fMRI_physio_8_decoder ok 74 74 33 150 1_dec08.dcm
19 fMRI_physio_9_decoder ok 74 74 33 150 1_dec09.dcm
21 fMRI_physio_10_decoder ok 74 74 33 150 1_dec10.dcm
23 fMRI_physio_1_retinotopy ok 74 74 33 120 1_retino01.dcm
25 fMRI_physio_2_retinotopy ok 74 74 32 120 1_retino02.dcm
27 fMRI_physio_3_retinotopy ok 74 74 32 120 1_retino03.dcm
29 fMRI_physio_4_retinotopy ok 74 74 32 120 1_retino04.dcm
31 fMRI_physio_5_retinotopy ok 74 74 32 120 1_retino05.dcm
35 T1_MEMPRAGE ok 256 256 176 4 1_T1_MEMPRAGE_35.dcm
36 T1_MEMPRAGE ok 256 256 176 1 1_RMS.dcm
error reading "file4": illegal operation on a directory
while executing
"gets $FileId line"
(procedure "ReadSeqCfg" line 11)
invoked from within
"ReadSeqCfg $seqcfgfile"
invoked from within
"if { [info exists seqcfgfile] } {
set SeqCfgList [ReadSeqCfg $seqcfgfile];
}"
(file "/home/jbang/freesurfer//bin/unpacksdcmdir.tcl" line 1048)
This same error message appeared on both v4.5.0 and v5.3.0.
Do you have any clue to fix it?
Thank you for your help.
Best,
Ji Won Bang
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] unpacking error
Hi.
When I tried dcmunpack:
dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
$DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK
I had error:
ERROR: Flag -seqcfg unrecognized.
-src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ
/home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg
/home/jbang/Projects/replay/log//
So I tried:
dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
$DATA_DIR/$SUBJECT/bold_decode -fsfast -run 3 bold nii.gz f.nii.gz
Then it seems like it's doing its job. but takes long time.
If I use dcmunpack, should I put each run argument rather than using
numaris4-protocols.unpackcfg?
I'll be waiting for your reply.
Thank you.
Best,
Ji Won
2016-02-04 11:56 GMT-05:00 Douglas Greve :
> Hi Ji Won, can you try dcmunpack? Should take the same arguments
>
>
> On 2/4/16 10:28 AM, Ji Won Bang wrote:
>
> Dear. Freesurfer team.
>
> Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and
> v5.3.0.
>
> The command line is:
>
> unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ
> $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK
>
> And I get the error message:
>
> $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $
>
> /home/jbang/Projects/replay/log
> -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ
> /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg
> /home/jbang/Projects/replay/log//
>
> Wed Feb 3 18:12:41 EST 2016
>
> mri_convert -all-info
> ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion:
> $Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug
> 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23
> nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux
> PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC
> CompilerVersion: 30400
>
> cpu166.cabiatl.com
> Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14
> 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux
>
> Wed Feb 3 18:12:41 EST 2016
> Log File is
> /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log
> INFO: Logfile is
> /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log
> SkipMoCo 0
> Scanning source directory ...
> INFO: summary file is
> /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile
> INFO: status file is
> /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status
> Scanning directory Wed Feb 3 18:12:41 EST 2016
> mri_parse_sdcmdir --sortbyrun --d
> /home/jbang/Projects/replay/epi//replay01/DICOM/day1 --o
> /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile
> --status /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status
> 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34
> 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70
> 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100
> Done scanning Wed Feb 3 18:17:33 EST 2016
> --
> 2localizer ok 512 512 3 1 2_loc02.dcm
> 3 fMRI_physio_1_decoder ok 74 74 33 150 1_dec01.dcm
> 5 fMRI_physio_2_decoder ok 74 74 33 150 1_dec02.dcm
> 7 fMRI_physio_3_decoder ok 74 74 33 150 1_dec03.dcm
> 9 fMRI_physio_4_decoder ok 74 74 33 150 1_dec04.dcm
> 11 fMRI_physio_5_decoder ok 74 74 33 150 1_dec05.dcm
> 13 fMRI_physio_6_decoder ok 74 74 33 150 1_dec06.dcm
> 15 fMRI_physio_7_decoder ok 74 74 33 150 1_dec07.dcm
> 17 fMRI_physio_8_decoder ok 74 74 33 150 1_dec08.dcm
> 19 fMRI_physio_9_decoder ok 74 74 33 150 1_dec09.dcm
> 21 fMRI_physio_10_decoder ok 74 74 33 150 1_dec10.dcm
> 23 fMRI_physio_1_retinotopy ok 74 74 33 120 1_retino01.dcm
> 25 fMRI_physio_2_retinotopy ok 74 74 32 120 1_retino02.dcm
> 27 fMRI_physio_3_retinotopy ok 74 74 32 120 1_retino03.dcm
> 29 fMRI_physio_4_retinotopy ok 74 74 32 120 1_retino04.dcm
> 31 fMRI_physio_5_retinotopy ok 74 74 32 120 1_retino05.dcm
> 35 T1_MEMPRAGE ok 256 256 176 4 1_T1_MEMPRAGE_35.dcm
> 36 T1_MEMPRAGE ok 256 256 176 1 1_RMS.dcm
> error reading "file4": illegal operation on a directory
> while executing
> "gets $FileId line"
> (procedure "ReadSeqCfg" line 11)
> invoked from within
> "ReadSeqCfg $seqcfgfile"
> invoked from within
> "if { [info exists seqcfgfile] } {
> set SeqCfgList [ReadSeqCfg $seqcfgfile];
> }"
> (file "/home/jbang/freesurfer//bin/unpacksdcmdir.tcl" li
Re: [Freesurfer] unpacking error
Hi, again. I tried dcmunpack: dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/ -fsfast -run 3 bold nii f.nii It worked. Inside $DATA_DIR/$SUBJECT/bold/003/, I see only 2 files: f.nii f-infodump.dat On the instruction page ( http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough), it says that 3 files are generated. which are paradigm file, f.nii, fmc.nii Why don't I get paradigm file and fmc.nii? Thank you! Best, Ji Won 2016-02-04 13:42 GMT-05:00 Ji Won Bang : > Hi. > > When I tried dcmunpack: > dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ > $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK > > I had error: > ERROR: Flag -seqcfg unrecognized. > -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ > /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg > /home/jbang/Projects/replay/log// > > So I tried: > dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ > $DATA_DIR/$SUBJECT/bold_decode -fsfast -run 3 bold nii.gz f.nii.gz > > Then it seems like it's doing its job. but takes long time. > > If I use dcmunpack, should I put each run argument rather than using > numaris4-protocols.unpackcfg? > > I'll be waiting for your reply. > > Thank you. > > Best, > Ji Won > > 2016-02-04 11:56 GMT-05:00 Douglas Greve : > >> Hi Ji Won, can you try dcmunpack? Should take the same arguments >> >> >> On 2/4/16 10:28 AM, Ji Won Bang wrote: >> >> Dear. Freesurfer team. >> >> Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and >> v5.3.0. >> >> The command line is: >> >> unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ >> $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK >> >> And I get the error message: >> >> $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ >> >> /home/jbang/Projects/replay/log >> -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ >> /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg >> /home/jbang/Projects/replay/log// >> >> Wed Feb 3 18:12:41 EST 2016 >> >> mri_convert -all-info >> ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: >> $Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug >> 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 >> nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux >> PlatformVersion: 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC >> CompilerVersion: 30400 >> >> cpu166.cabiatl.com >> Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 >> 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux >> >> Wed Feb 3 18:12:41 EST 2016 >> Log File is >> /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log >> INFO: Logfile is >> /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log >> SkipMoCo 0 >> Scanning source directory ... >> INFO: summary file is >> /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile >> INFO: status file is >> /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status >> Scanning directory Wed Feb 3 18:12:41 EST 2016 >> mri_parse_sdcmdir --sortbyrun --d >> /home/jbang/Projects/replay/epi//replay01/DICOM/day1 --o >> /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile >> --status /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status >> 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 32 34 >> 36 38 40 42 44 46 48 50 52 54 56 58 60 62 64 66 68 70 >> 72 74 76 78 80 82 84 86 88 90 92 94 96 98 100 >> Done scanning Wed Feb 3 18:17:33 EST 2016 >> -- >> 2localizer ok 512 512 3 1 2_loc02.dcm >> 3 fMRI_physio_1_decoder ok 74 74 33 150 1_dec01.dcm >> 5 fMRI_physio_2_decoder ok 74 74 33 150 1_dec02.dcm >> 7 fMRI_physio_3_decoder ok 74 74 33 150 1_dec03.dcm >> 9 fMRI_physio_4_decoder ok 74 74 33 150 1_dec04.dcm >> 11 fMRI_physio_5_decoder ok 74 74 33 150 1_dec05.dcm >> 13 fMRI_physio_6_decoder ok 74 74 33 150 1_dec06.dcm >> 15 fMRI_physio_7_decoder ok 74 74 33 150 1_dec07.dcm >> 17 fMRI_physio_8_decoder ok 74 74 33 150 1_dec08.dcm >> 19 fMRI_physio_9_decoder ok 74 74 33 150 1_dec09.dcm >> 21 fMRI_physio_10_decoder ok 74 74 33 150 1_dec10.dcm >> 23 fMRI_physio_1_retinotopy ok 74 74 3
Re: [Freesurfer] unpacking error
Thank you! Best, Ji Won > On Feb 4, 2016, at 7:01 PM, Douglas Greve wrote: > > that is not generated when unpacking. It is generated when you run > preproc-sess > > >> On 2/4/16 6:09 PM, Ji Won Bang wrote: >> Hi, again. >> >> I tried dcmunpack: >> dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ $DATA_DIR/$SUBJECT/ >> -fsfast -run 3 bold nii f.nii >> >> It worked. >> >> Inside $DATA_DIR/$SUBJECT/bold/003/, I see only 2 files: f.nii f-infodump.dat >> >> On the instruction page >> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough), >> it says that 3 files are generated. which are paradigm file, f.nii, fmc.nii >> >> Why don't I get paradigm file and fmc.nii? >> >> Thank you! >> >> Best, >> Ji Won >> >> 2016-02-04 13:42 GMT-05:00 Ji Won Bang : >>> Hi. >>> >>> When I tried dcmunpack: >>> dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ >>> $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK >>> >>> I had error: >>> ERROR: Flag -seqcfg unrecognized. >>> -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ >>> /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg >>> /home/jbang/Projects/replay/log// >>> >>> So I tried: >>> dcmunpack -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ >>> $DATA_DIR/$SUBJECT/bold_decode -fsfast -run 3 bold nii.gz f.nii.gz >>> >>> Then it seems like it's doing its job. but takes long time. >>> >>> If I use dcmunpack, should I put each run argument rather than using >>> numaris4-protocols.unpackcfg? >>> >>> I'll be waiting for your reply. >>> >>> Thank you. >>> >>> Best, >>> Ji Won >>> >>> 2016-02-04 11:56 GMT-05:00 Douglas Greve : >>>> Hi Ji Won, can you try dcmunpack? Should take the same arguments >>>> >>>> >>>> On 2/4/16 10:28 AM, Ji Won Bang wrote: >>>>> Dear. Freesurfer team. >>>>> >>>>> Hi. Our lab tried to unpack DICOM files using both freesurfer v4.5.0 and >>>>>v5.3.0. >>>>> >>>>> The command line is: >>>>> >>>>> unpacksdcmdir -src $DATA_DIR/$SUBJECT/DICOM/day1 -targ >>>>> $DATA_DIR/$SUBJECT/bold_decode -fsfast -seqcfg $LOG_DIR/$UNPACK >>>>> >>>>> And I get the error message: >>>>> >>>>> $Id: unpacksdcmdir,v 1.19.2.2 2008/03/11 19:56:38 nicks Exp $ >>>>> >>>>> /home/jbang/Projects/replay/log >>>>> -src /home/jbang/Projects/replay/epi//replay01/DICOM/day1 -targ >>>>> /home/jbang/Projects/replay/epi//replay01/bold_decode -fsfast -seqcfg >>>>> /home/jbang/Projects/replay/log// >>>>> >>>>> Wed Feb 3 18:12:41 EST 2016 >>>>> >>>>> mri_convert -all-info >>>>> ProgramName: mri_convert ProgramArguments: -all-info ProgramVersion: >>>>> $Name: stable4 $ TimeStamp: 2016/02/03-23:12:41-GMT BuildTimeStamp: Aug >>>>> 11 2009 07:36:05 CVS: $Id: mri_convert.c,v 1.146.2.5 2009/04/08 18:40:23 >>>>> nicks Exp $ User: jbang Machine: cpu166.cabiatl.com Platform: Linux >>>>> PlatformVersion: >>>>> 2.6.32-358.6.2.el6.x86_64 CompilerName: GCC CompilerVersion: 30400 >>>>> >>>>> cpu166.cabiatl.com >>>>> Linux cpu166.cabiatl.com 2.6.32-358.6.2.el6.x86_64 #1 SMP Tue May 14 >>>>> 15:48:21 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux >>>>> >>>>> Wed Feb 3 18:12:41 EST 2016 >>>>> Log File is >>>>> /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log >>>>> INFO: Logfile is >>>>> /home/jbang/Projects/replay/epi//replay01/bold_decode/unpack.log >>>>> SkipMoCo 0 >>>>> Scanning source directory ... >>>>> INFO: summary file is >>>>> /home/jbang/Projects/replay/epi//replay01/bold_decode/dicomdir.sumfile >>>>> INFO: status file is >>>>> /home/jbang/Projects/replay/epi//replay01/bold_decode/parse.status >>>>> Scanning directory Wed Feb 3 18:12:41 EST 2016 >>>>> mri_parse_sdcmdir --sortbyrun --d >>>>> /home/jbang/Projects/
[Freesurfer] seq.info
Dear. Freesurfer team I used dcmunpack to convert DCM to nii. This command didn't generate seq.info (I couldn't find it). I'd like to create one by myself Do you know how I can check the scan parameters: sequencename nrows ncols nslcs rowpixelsize colpixelsize slcpixelsize ntrs TR I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info I can get sequencename, nrows, ncols... but then from where can I check the others? Thank you very much. Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] seq.info
If I use: unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info I can get sequencename, nrows, ncols, nslcs, ntrs, but how can I check the exact value of slcpixelsize? Thanks, Ji Won 2016-02-05 14:54 GMT-05:00 Ji Won Bang : > Dear. Freesurfer team > > I used dcmunpack to convert DCM to nii. > > This command didn't generate seq.info (I couldn't find it). > > I'd like to create one by myself > > Do you know how I can check the scan parameters: > sequencename > nrows > ncols > nslcs > rowpixelsize > colpixelsize > slcpixelsize > ntrs > TR > > I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir > -scanonly targetdir /scan.info > > I can get sequencename, nrows, ncols... but then from where can I check > the others? > > Thank you very much. > > Best, > Ji Won > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] seq.info
Or my guess is that this seq.info is not necessary for the further analysis.. so I can go ahead without it? Best, Ji Won 2016-02-05 15:06 GMT-05:00 Ji Won Bang : > If I use: > unpacksdcmdir -src dicomdir -targ targetdir -scanonly targetdir /scan.info > > I can get sequencename, nrows, ncols, nslcs, ntrs, but how can I check the > exact value of slcpixelsize? > > Thanks, > Ji Won > > 2016-02-05 14:54 GMT-05:00 Ji Won Bang : > >> Dear. Freesurfer team >> >> I used dcmunpack to convert DCM to nii. >> >> This command didn't generate seq.info (I couldn't find it). >> >> I'd like to create one by myself >> >> Do you know how I can check the scan parameters: >> sequencename >> nrows >> ncols >> nslcs >> rowpixelsize >> colpixelsize >> slcpixelsize >> ntrs >> TR >> >> I know that when I use: unpacksdcmdir -src dicomdir -targ targetdir >> -scanonly targetdir /scan.info >> >> I can get sequencename, nrows, ncols... but then from where can I check >> the others? >> >> Thank you very much. >> >> Best, >> Ji Won >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] error in motion correction
Dear. Freesurfer team. Hi. I'm using freesurfer 4.5 version. While doing the motion correction, an error occurred. the command I used: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 the error I have: /home/jbang/Projects/replay/epi/replay01/bold_retino 3dvolreg -verbose -dfile 025/fmc.mcdat -base 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] ++ Authored by: RW Cox *+ WARNING: If you are performing spatial transformations on an oblique dset, such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique on this and other oblique datasets in the same session. See 3dWarp -help for details. ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 degrees from plumb. ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees from plumb. ++ centers of base and input datasets are 9.09 mm apart ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD don't have same dimensions! Input: nx=74 ny=74 nz=32 Base: nx=74 ny=74 nz=33 ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. I think it's because the volume size is different. The volume size for bold_retino is: number of slices 32 The volume size for bold_decode: number of slices 33 What should I do to correct this error? Thank you for taking your time. Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error in motion correction
Dear. Freesurfer team. I'd appreciate any advice from you. When doing the motion correction, I'd like to align all EPI data(bold_retino) to the first EPI of target run(bold_decode/003). However, the number of slices for target run(33) and the number of slices(32) for input run(bold_retino) are different. When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun $DATA_DIR/$SUBJECT/bold_decode/003 Freesurfer says that: ** FATAL ERROR: perhaps you could make your datasets match? ERROR: 3dvolreg Invalid null command. These two kinds of run (bold_decode, bold_retino) were collected in one scan per subject, so the head position should not be too different... Do you have any suggestions for fixing this error? Should I do 3dWarp -deoblique? Thank you so much. Best, Ji Won 2016-02-08 16:30 GMT-05:00 Ji Won Bang : > Dear. Freesurfer team. > > Hi. > > I'm using freesurfer 4.5 version. > > While doing the motion correction, an error occurred. > > the command I used: > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun > $DATA_DIR/$SUBJECT/bold_decode/003 > > the error I have: > /home/jbang/Projects/replay/epi/replay01/bold_retino > 3dvolreg -verbose -dfile 025/fmc.mcdat -base > 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix > 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz > ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] > ++ Authored by: RW Cox > *+ WARNING: If you are performing spatial transformations on an oblique > dset, > such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, > or viewing/combining it with volumes of differing obliquity, > you should consider running: > 3dWarp -deoblique > on this and other oblique datasets in the same session. > See 3dWarp -help for details. > ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 > degrees from plumb. > ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz > ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 degrees > from plumb. > ++ centers of base and input datasets are 9.09 mm apart > ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD > don't have same dimensions! >Input: nx=74 ny=74 nz=32 >Base: nx=74 ny=74 nz=33 > ** FATAL ERROR: perhaps you could make your datasets match? > ERROR: 3dvolreg > Invalid null command. > > I think it's because the volume size is different. > > The volume size for bold_retino is: number of slices 32 > The volume size for bold_decode: number of slices 33 > > What should I do to correct this error? > > Thank you for taking your time. > > Best, > Ji Won > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error in motion correction
Dear. Freesurfer team. As another attempt, I run the motion correction without the argument -targrun: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino However, I get the same error message again. Why is that? Thanks so much for your effort and time. I appreciate it a lot. Best, Ji Won 2016-02-08 17:16 GMT-05:00 Ji Won Bang : > Dear. Freesurfer team. > > I'd appreciate any advice from you. > > When doing the motion correction, I'd like to align all EPI > data(bold_retino) to the first EPI of target run(bold_decode/003). However, > the number of slices for target run(33) and the number of slices(32) for > input run(bold_retino) are different. > > When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino > -targrun $DATA_DIR/$SUBJECT/bold_decode/003 > > Freesurfer says that: > ** FATAL ERROR: perhaps you could make your datasets match? > ERROR: 3dvolreg > Invalid null command. > > These two kinds of run (bold_decode, bold_retino) were collected in one > scan per subject, so the head position should not be too different... > > Do you have any suggestions for fixing this error? > > Should I do 3dWarp -deoblique? > > Thank you so much. > > Best, > Ji Won > > 2016-02-08 16:30 GMT-05:00 Ji Won Bang : > >> Dear. Freesurfer team. >> >> Hi. >> >> I'm using freesurfer 4.5 version. >> >> While doing the motion correction, an error occurred. >> >> the command I used: >> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun >> $DATA_DIR/$SUBJECT/bold_decode/003 >> >> the error I have: >> /home/jbang/Projects/replay/epi/replay01/bold_retino >> 3dvolreg -verbose -dfile 025/fmc.mcdat -base >> 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix >> 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz >> ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] >> ++ Authored by: RW Cox >> *+ WARNING: If you are performing spatial transformations on an oblique >> dset, >> such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, >> or viewing/combining it with volumes of differing obliquity, >> you should consider running: >> 3dWarp -deoblique >> on this and other oblique datasets in the same session. >> See 3dWarp -help for details. >> ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 >> degrees from plumb. >> ++ Reading in base dataset 025/tmp.mc-afni2.32291/tempvol.nii.gz >> ++ Oblique dataset:025/tmp.mc-afni2.32291/invol.nii.gz is 4.564286 >> degrees from plumb. >> ++ centers of base and input datasets are 9.09 mm apart >> ** Input ./invol.nii.gz+orig.HEAD and base ./tempvol.nii.gz+orig.HEAD >> don't have same dimensions! >>Input: nx=74 ny=74 nz=32 >>Base: nx=74 ny=74 nz=33 >> ** FATAL ERROR: perhaps you could make your datasets match? >> ERROR: 3dvolreg >> Invalid null command. >> >> I think it's because the volume size is different. >> >> The volume size for bold_retino is: number of slices 32 >> The volume size for bold_decode: number of slices 33 >> >> What should I do to correct this error? >> >> Thank you for taking your time. >> >> Best, >> Ji Won >> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error in motion correction
Dear. Freesurfer team. Thanks so much your help and advice. Based on the comments, I'm trying freesurfer version 5.3.0 instead of 4.5.0 now. In our experiment, each participant is scanned twice on different days and the functional scan's brain volume are different (some scans have 33 number of slices, some have 32 number of slices). Since participants moved a bit between scans on the same day, and the head position is different between different days, my advisor advised me to do co-registration between different functional scans and then do co-registration between anatomical and functional scans. My question is this. If I do motion-correction such that we align all EPI data to the first EPI of the first functional scan, will it be enough for co-registration between different functional scans and different days? Or should I do coregistration-specific process such as mri_robust_register, mri_robust_template etc? Or I guess the method I choose should depend on how much the participant moved between scans and how much different the head position was between different days? For example, if the participant was very still between runs and the head position was not that too different, this motion correction is enough for coregistration between functional scans. However, if not, I should do coregistration-specific process such as mri_robust_register, mri_robust_template etc? I'd appreciate any of your advice. Please feel free to let me know your thoughts. Best, Ji Won 2016-02-08 22:31 GMT-05:00 Douglas Greve : > In 4.5 I don't think there is a way to run it when different runs have > different number of slices. Version 5+ will handle it properly. If you > really want to use 4.5, then you'll have to put it in a different > functional subdir (FSD, eg, bold), and create a new analysis for it, then > combine them together after analysis. A bit of a hassle. > > > On 2/8/16 5:58 PM, Ji Won Bang wrote: > > Dear. Freesurfer team. > > As another attempt, I run the motion correction without the argument > -targrun: > > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino > > However, I get the same error message again. > > Why is that? > > Thanks so much for your effort and time. > > I appreciate it a lot. > > Best, > Ji Won > > > 2016-02-08 17:16 GMT-05:00 Ji Won Bang : > >> Dear. Freesurfer team. >> >> I'd appreciate any advice from you. >> >> When doing the motion correction, I'd like to align all EPI >> data(bold_retino) to the first EPI of target run(bold_decode/003). However, >> the number of slices for target run(33) and the number of slices(32) for >> input run(bold_retino) are different. >> >> When I type: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino >> -targrun $DATA_DIR/$SUBJECT/bold_decode/003 >> >> Freesurfer says that: >> ** FATAL ERROR: perhaps you could make your datasets match? >> ERROR: 3dvolreg >> Invalid null command. >> >> These two kinds of run (bold_decode, bold_retino) were collected in one >> scan per subject, so the head position should not be too different... >> >> Do you have any suggestions for fixing this error? >> >> Should I do 3dWarp -deoblique? >> >> Thank you so much. >> >> Best, >> Ji Won >> >> 2016-02-08 16:30 GMT-05:00 Ji Won Bang < >> kirsten...@gmail.com>: >> >>> Dear. Freesurfer team. >>> >>> Hi. >>> >>> I'm using freesurfer 4.5 version. >>> >>> While doing the motion correction, an error occurred. >>> >>> the command I used: >>> mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -targrun >>> $DATA_DIR/$SUBJECT/bold_decode/003 >>> >>> the error I have: >>> /home/jbang/Projects/replay/epi/replay01/bold_retino >>> 3dvolreg -verbose -dfile 025/fmc.mcdat -base >>> 025/tmp.mc-afni2.32291/tempvol.nii.gz -prefix >>> 025/tmp.mc-afni2.32291/outvol.nii.gz 025/tmp.mc-afni2.32291/invol.nii.gz >>> ++ 3dvolreg: AFNI version=AFNI_2008_07_18_1710 (Feb 10 2009) [64-bit] >>> ++ Authored by: RW Cox >>> *+ WARNING: If you are performing spatial transformations on an >>> oblique dset, >>> such as 025/tmp.mc-afni2.32291/tempvol.nii.gz, >>> or viewing/combining it with volumes of differing obliquity, >>> you should consider running: >>> 3dWarp -deoblique >>> on this and other oblique datasets in the same session. >>> See 3dWarp -help for details. >>> ++ Oblique dataset:025/tmp.mc-afni2.32291/tempvol.nii.gz is 3.263868 >>> degrees from plumb. >>> ++ Reading in base dataset 0
[Freesurfer] error in mc-sess
Dear. freesurfer experts. Hi. I'm using freesurfer version 5.3.0. I tried mc-sess onto runs that have different number of slices. However, due to this different number of slices in different runs, mc-sess gives an error. I expected that running mc-sess in freesurfer version 5.3.0 would handle this issue. If you can share your idea to fix this problem, that would be a great help. Thank you! Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error in mc-sess
The command I used is: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session Thank you. Best, Ji Won 2016-03-03 12:22 GMT-05:00 Ji Won Bang : > Dear. freesurfer experts. > > Hi. I'm using freesurfer version 5.3.0. > > I tried mc-sess onto runs that have different number of slices. > > However, due to this different number of slices in different runs, mc-sess > gives an error. > > I expected that running mc-sess in freesurfer version 5.3.0 would handle > this issue. > > If you can share your idea to fix this problem, that would be a great help. > > Thank you! > > Best, > Ji Won > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] error in mc-sess
Thanks for your reply. It works. I have 1 more general question. When running: mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 I get 2 files (template.log & template.nii.gz) under the functional subdirectory(bold_day1) and under each run(001, 002 etc). When I run: mc-sess -s $SUBJECT -df sessdirfile -fsd bold_day1 -per-run Does that command use the template for motion correction that was created under each run? Not the one under the functional subdirectory? My understanding of mktemplate-sess and mc-sess is that mktemplate-sess produces the template per each run (saves the template file under each run) and/or the template per session(?) (saves the template file under the functional subdirectory). Then mc-sess utilizes the template for motion correction. If I use -per-run, mc-sess utilizes the template file created per each run and if I use -per-session, mc-see utilizes the template file created per session(file under the functional subdirectory). Is my understanding correct? Thanks a lot! Best, Ji Won 2016-03-03 12:36 GMT-05:00 Douglas N Greve : > you have to use -per-run not -per-session > > > On 03/03/2016 12:27 PM, Ji Won Bang wrote: > > The command I used is: > > > > mktemplate-sess -s $SUBJECT -df sessdirfile -fsd bold_retino > > > > mc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-session > > > > Thank you. > > > > Best, > > Ji Won > > > > > > > > 2016-03-03 12:22 GMT-05:00 Ji Won Bang > <mailto:kirsten...@gmail.com>>: > > > > Dear. freesurfer experts. > > > > Hi. I'm using freesurfer version 5.3.0. > > > > I tried mc-sess onto runs that have different number of slices. > > > > However, due to this different number of slices in different runs, > > mc-sess gives an error. > > > > I expected that running mc-sess in freesurfer version 5.3.0 would > > handle this issue. > > > > If you can share your idea to fix this problem, that would be a > > great help. > > > > Thank you! > > > > Best, > > Ji Won > > > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mkbrainmask-sess and inorm-sess
Dear. Freesurfer experts. Hi. How are you? It might be very naive question. When using version 4.5.0 I used the command: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino However under the version 5.3.0, mkbrainmask-sess does not have -funcstem. May I use -maskstem instead of -funcstem? If so, after that, I tried: inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd bold_retino However, it complains that: ERROR: cannot find /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain You may need to run preproc-sess or mkbrainmask-sess to create a brain mask Could you please help? Thank you very much. Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mkbrainmask-sess and inorm-sess
In a simple word, my question is: under version 5.3.0, how can I specify funcstem (stem of functional volume)? I don't see any argument for that.. Thanks a lot. Best, Ji Won 2016-03-04 16:31 GMT-05:00 Ji Won Bang : > Dear. Freesurfer experts. > > Hi. How are you? > > It might be very naive question. > > When using version 4.5.0 I used the command: > mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino > > However under the version 5.3.0, mkbrainmask-sess does not have -funcstem. > > May I use -maskstem instead of -funcstem? > > If so, after that, I tried: > inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd > bold_retino > > However, it complains that: > ERROR: cannot find > /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain > You may need to run preproc-sess or mkbrainmask-sess to create a brain mask > > Could you please help? > > Thank you very much. > > Best, > Ji Won > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mkbrainmask-sess and inorm-sess
Thanks for your help! I'd like to run mkbrainmask-sess & inorm-sess under version 5.3.0 What I used to run are: mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd bold_retino inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd bold_retino However, since version 5.3.0 changed a lot, I tried: mkbrainmask-sess -s $SUBJECT -df sessdirfile -fsd bold_retino inorm-sess -s $SUBJECT -motioncor -df sessdirfile -fsd bold_retino It gives me an error: ERROR: could not determine file for /home/jbang/Projects/replay/epi/replay06/bold_retino/023/fmc ERROR: inorm failed Which part am I doing wrong? Thank you so much. Best, Ji Won 2016-03-04 17:13 GMT-05:00 Douglas N Greve : > The functional stream changed a lot from version 4 to version 5. The > commands and workflow are very different now > > On 03/04/2016 04:31 PM, Ji Won Bang wrote: > > Dear. Freesurfer experts. > > > > Hi. How are you? > > > > It might be very naive question. > > > > When using version 4.5.0 I used the command: > > mkbrainmask-sess -s $SUBJECT -funcstem fmc -df sessdirfile -fsd > > bold_retino > > > > However under the version 5.3.0, mkbrainmask-sess does not have > -funcstem. > > > > May I use -maskstem instead of -funcstem? > > > > If so, after that, I tried: > > inorm-sess -s $SUBJECT -motioncor -funcstem fmc -df sessdirfile -fsd > > bold_retino > > > > However, it complains that: > > ERROR: cannot find > > /home/jbang/Projects/replay/epi/replay06/bold_retino/masks/brain > > You may need to run preproc-sess or mkbrainmask-sess to create a brain > > mask > > > > Could you please help? > > > > Thank you very much. > > > > Best, > > Ji Won > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] [freesurfer] selxavg-sess question
Dear. Freesurfer experts. Hi. I'm using freesurfer version 5.3.0. I tried: mkanalysis-sess -analysis retino -TR 2 -paradigm para.para -event-related -funcstem fmc -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25 -polyfit 2 -mcextreg -force -fsd bold_retino -per-run -native -refeventdur 8 mkcontrast-sess -analysis retino -contrast HorVer -a 1 -c 2 preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -nosmooth -per-run selxavg-sess -s $SUBJECT -analysis retino -df sessdirfile -noomnibus Then at the selxavg-sess process, I got the error: INFO: WhitenFlag = 0 -- selxavg-sess logfile is /home/jbang/Projects/replay/log/log/selxavg-sess-bold_retino-retino-160308143510.log -- --- /home/jbang/Projects/replay/epi/replay06 Tue Mar 8 14:35:10 EST 2016 ERROR: could not find volume ERROR:. Does it exist? (standard_in) 1: syntax error ERROR: could not find volume ERROR:. Does it exist? inplaneres TR INFO (replay06): RunList = 023 025 027 029 /home/jbang/Projects/replay/epi/replay06/bold_retino selxavg2 -TR -parname para.para -o retino/h -i 023/fmc -i 025/fmc -i 027/fmc -i 029/fmc -cfg /home/jbang/Projects/replay/log/retino/analysis.cfg --- Parsing Config File: /home/jbang/Projects/replay/log/retino/analysis.cfg -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 ERROR: Flag 3 unrecognized. -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 -TR -parname para.para -o retino/h -i 023/fmc -i 025/fmc -i 027/fmc -i 029/fmc -cfg /home/jbang/Projects/replay/log/retino/analysis.cfg ERROR (/home/jbang/Projects/replay/epi/replay06): selxavg failed Could you please hlep what's going wrong? Thank you very much! Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] [freesurfer] selxavg-sess question
Dear. Experts. I appreciate your help in advance. I also tried: selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile Then I got the error: - selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino-160308154755.log -- --- /home/jbang/Projects/replay/epi/replay06 Tue Mar 8 15:47:56 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/jbang/Projects/replay/log >> sxa3cmd = /usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino -df sessdirfile >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# replay06 ### /home/jbang/Projects/replay/epi/replay06 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/jbang/Projects/replay/epi Extension format = nii.gz 1 HorVer.mat 2 UpperLower.mat ??? Error using ==> MRIread at 76 ERROR: cannot determine format of /home/jbang/Projects/replay/epi/replay06/bold_retino/023/fmc (MRIread) Error in ==> flac_customize at 87 mri = MRIread(fstem,1); Error in ==> fast_selxavg3 at 65 flac0 = flac_customize(flac0); >> -- ERROR: fast_selxavg3() failed\n Could you please help? Before running this, I run preproc-sess. Thank you. Best, Ji Won 2016-03-08 14:41 GMT-05:00 Ji Won Bang : > Dear. Freesurfer experts. > > Hi. > > I'm using freesurfer version 5.3.0. > > I tried: > > mkanalysis-sess -analysis retino -TR 2 -paradigm para.para -event-related > -funcstem fmc -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25 > -polyfit 2 -mcextreg -force -fsd bold_retino -per-run -native -refeventdur 8 > > mkcontrast-sess -analysis retino -contrast HorVer -a 1 -c 2 > > preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -nosmooth > -per-run > > selxavg-sess -s $SUBJECT -analysis retino -df sessdirfile -noomnibus > > Then at the selxavg-sess process, I got the error: > > INFO: WhitenFlag = 0 > -- > selxavg-sess logfile is > /home/jbang/Projects/replay/log/log/selxavg-sess-bold_retino-retino-160308143510.log > -- > --- > /home/jbang/Projects/replay/epi/replay06 > Tue Mar 8 14:35:10 EST 2016 > ERROR: could not find volume ERROR:. Does it exist? > (standard_in) 1: syntax error > ERROR: could not find volume ERROR:. Does it exist? > inplaneres > TR > INFO (replay06): RunList = 023 025 027 029 > > /home/jbang/Projects/replay/epi/replay06/bold_retino > selxavg2 -TR -parname para.para -o retino/h -i 023/fmc -i 025/fmc -i > 027/fmc -i 029/fmc -cfg /home/jbang/Projects/replay/log/retino/analysis.cfg > > --- Parsing Config File: > /home/jbang/Projects/replay/log/retino/analysis.cfg > -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 > -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 > ERROR: Flag 3 unrecognized. > -gammafit 2.25 1.25 -timewindow 34 -prestim 0 -polyfit 2 -TER 2 -nskip 0 > -fwhm 0 -extreg mcextreg -nextreg 3 -rescale 1000 -TR -parname para.para -o > retino/h -i 023/fmc -i 025/fmc -i 027/fmc -i 029/fmc -cfg > /home/jbang/Projects/replay/log/retino/analysis.cfg > ERROR (/home/jbang/Projects/replay/epi/replay06): selxavg failed > > Could you please hlep what's going wrong? > > Thank you very much! > > Best, > Ji Won > ___ Freesurfer mailing list F
[Freesurfer] selxavg3-sess question
Dear. Freesurfer experts. Hi. i appreciate your help in advance! I'm using freesurfer version 5.3.0. I tried selxavg3-sess and got the error dimension mismatch between mask and 2th run. Actually, the number of slices of the 1st run and the rest are different. Is it the reason why I get this error message? Please let me know what I should do to correct this error! Below are command and error lines. command: selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile error: -- selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino-160309115326.log -- --- /home/jbang/Projects/replay/epi/replay06 Wed Mar 9 11:53:33 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/jbang/Projects/replay/log >> sxa3cmd = /usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino -df sessdirfile >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# replay06 ### /home/jbang/Projects/replay/epi/replay06 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/jbang/Projects/replay/epi Extension format = nii.gz 1 HorVer.mat 2 UpperLower.mat nruns = 4 autostimdur = outanadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino Found 62211/180708 (34.4) voxels in mask Creating Design Matrix ... creation time = 0.008 sec DoMCFit = 0 ntptot = 480, nX = 28, DOF = 452 Saving X matrix to /home/jbang/Projects/replay/epi/replay06/bold_retino/retino/Xtmp.mat XCond = 199.451 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.499283(t=0.024843) 2 -0.25 -0.268756(t=0.047925) 3 0 -0.0441607(t=0.069497) 4 0.25 0.16942(t=0.093633) 5 0.5 0.359032(t=0.117433) AR1 Correction M: 0.0657489 1.15858 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 855.07 run 2t= 3.1 ERROR: dimension mismatch between mask and 2th run >> -- ERROR: fast_selxavg3() failed\n Thank you very much! Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] selxavg3-sess question
Dear. Freesurfer experts. Hi. I'm pretty sure that this error is due to the different number of slices in different runs I ran preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_Retino -nosmmth -per-run -force Then I ran selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile I thought preproc-sess -per-run creates mask for each run.. but probably not... Could you please advise me how to correct this dimension mismatch between mask and 2th run? Thank you very much! Best, Ji Won 2016-03-09 12:08 GMT-05:00 Ji Won Bang : > Dear. Freesurfer experts. > > Hi. > > i appreciate your help in advance! > > I'm using freesurfer version 5.3.0. > > I tried selxavg3-sess and got the error dimension mismatch between mask > and 2th run. > Actually, the number of slices of the 1st run and the rest are different. > Is it the reason why I get this error message? > Please let me know what I should do to correct this error! > > Below are command and error lines. > > command: selxavg3-sess -s $SUBJECT -analysis retino -df sessdirfile > > error: > -- > selxavg3-sess logfile is > /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino-160309115326.log > -- > --- > /home/jbang/Projects/replay/epi/replay06 > Wed Mar 9 11:53:33 EST 2016 > anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino > DoGLMFit = 1 > DoContrasts = 1 > UpdateNeeded = 1 > -- > --- matlab output > Warning: Unable to open display 'iconic'. You will not be able to display > graphics on the screen. > > < M A T L A B (R) > > Copyright 1984-2009 The MathWorks, Inc. > Version 7.8.0.347 (R2009a) 64-bit (glnxa64) > February 12, 2009 > > > To get started, type one of these: helpwin, helpdesk, or demo. > For product information, visit www.mathworks.com. > > >> >> >> >> >> >> >> > sxa3pwd = > > /home/jbang/Projects/replay/log > > >> > sxa3cmd = > > /usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis > retino -df sessdirfile > > >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> > > #@# replay06 ### > /home/jbang/Projects/replay/epi/replay06 > - > $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ > /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m > /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m > /usr/local/freesurfer/matlab/MRIread.m > - > outtop = /home/jbang/Projects/replay/epi > Extension format = nii.gz > 1 HorVer.mat > 2 UpperLower.mat > nruns = 4 > autostimdur = > > > outanadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino > Found 62211/180708 (34.4) voxels in mask > Creating Design Matrix > ... creation time = 0.008 sec > DoMCFit = 0 > ntptot = 480, nX = 28, DOF = 452 > Saving X matrix to > /home/jbang/Projects/replay/epi/replay06/bold_retino/retino/Xtmp.mat > XCond = 199.451 (normalized) > Computing compensation for resdual AR1 bias > 1 -0.5 -0.499283(t=0.024843) > 2 -0.25 -0.268756(t=0.047925) > 3 0 -0.0441607(t=0.069497) > 4 0.25 0.16942(t=0.093633) > 5 0.5 0.359032(t=0.117433) > AR1 Correction M: 0.0657489 1.15858 > Computing contrast matrices > OLS Beta Pass > run 1t= 0.0 > Global Mean 855.07 > run 2t= 3.1 > ERROR: dimension mismatch between mask and 2th run > >> -- > ERROR: fast_selxavg3() failed\n > > Thank you very much! > > Best, > Ji Won > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] question about selxavg3-sess
Dear. Freesurfer experts. Hi. I'm trying retinotopy analysis using freesurfer version 5.3.0. I'm having a problem when running selxavg3-sess... Could you please help me with this issue? I have 3 runs under bold_retino and all 3 scans have the same dimension.. The command line that I entered are: mkanalysis-sess -analysis retino.lh -TR 2 -paradigm para.para -event-related -funcstem fmcpr.sm0.self.lh -nconditions 4 -timewindow 34 -inorm -gammafit 2.25 1.25 -polyfit 2 -nuisreg mcprextreg 3 -force -fsd bold_retino -per-run -surface self lh -refeventdur 8 mkcontrast-sess -analysis retino.lh -contrast HorVer -a 1 -c 2 mkcontrast-sess -analysis retino.lh -contrast UpperLower -a 3 -c 4 preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_retino -per-run -force -surface self lhrh -fwhm 0 selxavg3-sess -s $SUBJECT -analysis retino.lh -df sessdirfile Then I get the error: Surface data self lh -- selxavg3-sess logfile is /home/jbang/Projects/replay/log/log/selxavg3-sess-bold_retino-retino.lh-160310164355.log -- --- /home/jbang/Projects/replay/epi/replay06 Thu Mar 10 16:43:56 EST 2016 anadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh DoGLMFit = 1 DoContrasts = 1 UpdateNeeded = 1 -- --- matlab output Warning: Unable to open display 'iconic'. You will not be able to display graphics on the screen. < M A T L A B (R) > Copyright 1984-2009 The MathWorks, Inc. Version 7.8.0.347 (R2009a) 64-bit (glnxa64) February 12, 2009 To get started, type one of these: helpwin, helpdesk, or demo. For product information, visit www.mathworks.com. >> >> >> >> >> >> >> sxa3pwd = /home/jbang/Projects/replay/log >> sxa3cmd = /usr/local/freesurfer//fsfast/bin/selxavg3-sess -s replay06 -analysis retino.lh -df sessdirfile >> /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> #@# replay06 ### /home/jbang/Projects/replay/epi/replay06 - $Id: fast_selxavg3.m,v 1.100.2.2 2012/11/30 18:40:38 greve Exp $ /usr/local/freesurfer/fsfast/toolbox/fast_selxavg3.m /usr/local/freesurfer/fsfast/toolbox/fast_ldanaflac.m /usr/local/freesurfer/matlab/MRIread.m - outtop = /home/jbang/Projects/replay/epi Extension format = nii.gz 1 HorVer.mat 2 UpperLower.mat nruns = 3 autostimdur = outanadir = /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh Found 140089/148112 (94.6) voxels in mask Creating Design Matrix ... creation time = 0.007 sec DoMCFit = 1 ntptot = 360, nX = 22, DOF = 338 Saving X matrix to /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/Xtmp.mat XCond = 200.812 (normalized) Computing compensation for resdual AR1 bias 1 -0.5 -0.500111(t=0.013194) 2 -0.25 -0.270166(t=0.024429) 3 0 -0.0463709(t=0.035203) 4 0.25 0.166079(t=0.04517) 5 0.5 0.354234(t=0.055571) AR1 Correction M: 0.0689761 1.16382 Computing contrast matrices OLS Beta Pass run 1t= 0.0 Global Mean 862.23 run 2t= 2.0 Global Mean 864.13 run 3t= 4.1 Global Mean 864.40 Global In-Mask Mean = 863.588 (889.887) Rescale Target = 100 RescaleFactor = 0.115796 OLS Residual Pass run 1t= 0.0 Saving rho1 run 2t= 3.4 Saving rho1 run 3t= 7.1 Saving rho1 Smoothing ACF /usr/local/freesurfer//bin/mris_fwhm --mask /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/mask.nii.gz --i /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.nii.gz --o /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only --s replay06 --hemi lh --sd /home/jbang/Projects/replay/mri/ /usr/local/freesurfer//bin/mris_fwhm: /usr/local/matlab.r2009a/sys/os/glnxa64/libstdc++.so.6: version `GLIBCXX_3.4.11' not found (required by /usr/local/freesurfer//bin/mris_fwhm) ERROR: /usr/local/freesurfer//bin/mris_fwhm --mask /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/mask.nii.gz --i /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.nii.gz --o /home/jbang/Projects/replay/epi/replay06/bold_retino/retino.lh/rho1mn.sm.nii.gz --fwhm 20.00 --smooth-only --s replay06 --hemi lh --sd /home/jbang/Projects/replay/mri/ >> -- ERROR: fast_selxavg3() failed\n I'm getting confused what's causing this issue. Please help! I appreciate your advice in advance. Thanks, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person
[Freesurfer] mri_robust_register question
Dear. All. Hi. How are you? It might be a very naive question, but your advice is greatly appreciated! I'm trying to register 2 T1s obtained from 1 subject on different days and then register the functional scans to their corresponding T1s (registering the functional scans to the same day's T1). By doing so, I expect to get everything into the same space. (Each subject was scanned twice on two different days etc., day1 and day2) After running mri_robust_register onto day2's T1 as targetting day1's T1, I get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run preproc-sess(that does registration as well) onto day2's functional scans. Is there a way to make preproc-sess do register functional scans of day2 to v2to1.mgz(of day2 that's created by mri_robust_register), not the original 046.mgz? The commands that I run are: recon-all -s $SUBJECT -all mri_robust_register --mov /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz --iscale --satit preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force -fwhm 0 Please feel free to give me any advice! Thank you very much. Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_robust_register question
Hi. Daniel. How are you? Thanks for your reply. That should be another option for me! Thanks, Ji Won 2016-03-17 15:16 GMT-04:00 dgw : > Hi Ji-Won, > > Why not just input both T1s to recon-all it will motion correct and > average and then all of your functionals will be registered to the > same FS data? > > hth > d > > On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang wrote: > > Dear. All. > > > > Hi. How are you? > > > > It might be a very naive question, but your advice is greatly > appreciated! > > > > I'm trying to register 2 T1s obtained from 1 subject on different days > and > > then register the functional scans to their corresponding T1s > (registering > > the functional scans to the same day's T1). By doing so, I expect to get > > everything into the same space. > > > > (Each subject was scanned twice on two different days etc., day1 and > day2) > > > > After running mri_robust_register onto day2's T1 as targetting day1's > T1, I > > get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run > > preproc-sess(that does registration as well) onto day2's functional > scans. > > > > Is there a way to make preproc-sess do register functional scans of day2 > to > > v2to1.mgz(of day2 that's created by mri_robust_register), not the > original > > 046.mgz? > > > > The commands that I run are: > > > > recon-all -s $SUBJECT -all > > > > mri_robust_register --mov > > /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst > > /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta > > /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov > > /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights > > /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz > --iscale > > --satit > > > > preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run -force > > -fwhm 0 > > > > Please feel free to give me any advice! > > > > Thank you very much. > > > > Best, > > Ji Won > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > > e-mail > > contains patient information, please contact the Partners Compliance > > HelpLine at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in > > error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mris_flatten error: bad vertex
Dear. Freesurfer experts. Hi. I'm having a problem with mris_flatten (version 5.3.0) Could you please help me fix this problem? My command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat It returns the error: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d with 30434 vertices (20.5% of total) MRISreadPatch: bad vertex # (148517) found in patch file No such file or directory When making the patch lh.oc.patch.3d, I followed the processes below: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast UpperLower select 3 points along a boundary between upper and lower visual fields (near calcarine sulcus) and press "Cut line". Then, select 4 points to define the cutting plane: 1 on lower side of the line, 2 on upper side of the line, 3 on the opposite surface (use rotation tool), and 4 to specify which portion of surface is kept, and press "Cur plane". File->Patch->Save Patch As lh.oc.patch.3d So I think I made the patch correctly. ! weird thing that I suspect is that when I click save patch as, the default location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to $SUBJECTS_DIR/$SUBJECT/surf Could you please help me? Thanks a lot! Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] preproc-sess in longitudinal stream
Dear. Freesurfer experts. Hi. How are you? I have dataset where a single subject was scanned twice on different days. I ran recon-all in logitudinal stream (cross, base, long). The recon-all -base gave me the within-subject template and the recon-all -long gave me the directory in the format of tp1id.long.templateID. By doing so, I get different time point's norm.mgz (under tp1id.long.templateID directory and tp2id.long.templateID etc) aligned in the same voxel space. As a next step, I'd like to register the functional scans to the anatomical scans via preproc-sess (or mc-sess, spmregister-sess etc). I guess, the anatomical can that I should use is norm.mgz under tp1id.long.templateID directory and tp2id.long.templateID etc. (?) To register the functional scans to the newly created anatomical image obtained from recon-all -long process (norm.mgz under tp1id.long.templateID directory and tp2id.long.templateID etc), I think I should specify this newly created norm.mgz in the command line... but couldn't figure it out yet. The preproc-sess command that I used in the cross-sectional process is as below: preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_decode -per-run -force -fwhm 0 What should I do to make registration process target a specific anatomical image? Please give me any advice! Thank you so much for your help! Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_robust_register question
Thank you for your reply! I'll take a look at the longitudinal stream tutorial. Best, Ji Won 2016-03-17 15:56 GMT-04:00 Martin Reuter : > Hi, > > when using recon-all for this, the right way would be to run both images > through the longitudinal stream. This will create a mid-space template > and map both time points to it. That space can also be used as target > for the functional data. That way you stay unbiased. > > Probably the potential processing bias is small for this kind of > analysis, so you can also probably get away with using the first time > point structural space for everything. I am not familiar with the > preproc-sess command to give advice. But there are others on this list > who know. > > Best, Martin > > On 03/17/2016 03:16 PM, dgw wrote: > > Hi Ji-Won, > > > > Why not just input both T1s to recon-all it will motion correct and > > average and then all of your functionals will be registered to the > > same FS data? > > > > hth > > d > > > > On Thu, Mar 17, 2016 at 3:06 PM, Ji Won Bang > wrote: > >> Dear. All. > >> > >> Hi. How are you? > >> > >> It might be a very naive question, but your advice is greatly > appreciated! > >> > >> I'm trying to register 2 T1s obtained from 1 subject on different days > and > >> then register the functional scans to their corresponding T1s > (registering > >> the functional scans to the same day's T1). By doing so, I expect to get > >> everything into the same space. > >> > >> (Each subject was scanned twice on two different days etc., day1 and > day2) > >> > >> After running mri_robust_register onto day2's T1 as targetting day1's > T1, I > >> get v2to1.mgz (original T1 is 046.mgz). Then I'd like to run > >> preproc-sess(that does registration as well) onto day2's functional > scans. > >> > >> Is there a way to make preproc-sess do register functional scans of > day2 to > >> v2to1.mgz(of day2 that's created by mri_robust_register), not the > original > >> 046.mgz? > >> > >> The commands that I run are: > >> > >> recon-all -s $SUBJECT -all > >> > >> mri_robust_register --mov > >> /home/jbang/Projects/replay/mri/replay10/mri/orig/046.mgz --dst > >> /home/jbang/Projects/replay/mri/replay06/mri/orig/036.mgz --lta > >> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.lta --mapmov > >> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1.mgz --weights > >> /home/jbang/Projects/replay/mri/replay10/mri/orig/v2to1-weights.mgz > --iscale > >> --satit > >> > >> preproc-sess -s $SUBJECT -df sessdirfile -fsd bold_sponta -per-run > -force > >> -fwhm 0 > >> > >> Please feel free to give me any advice! > >> > >> Thank you very much. > >> > >> Best, > >> Ji Won > >> > >> > >> ___ > >> Freesurfer mailing list > >> Freesurfer@nmr.mgh.harvard.edu > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> > >> > >> The information in this e-mail is intended only for the person to whom > it is > >> addressed. If you believe this e-mail was sent to you in error and the > >> e-mail > >> contains patient information, please contact the Partners Compliance > >> HelpLine at > >> http://www.partners.org/complianceline . If the e-mail was sent to you > in > >> error > >> but does not contain patient information, please contact the sender and > >> properly > >> dispose of the e-mail. > >> > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > -- > Martin Reuter, PhD > Assistant Professor of Radiology, Harvard Medical School > Assistant Professor of Neurology, Harvard Medical School > A.A.Martinos Center for Biomedical Imaging > Massachusetts General Hospital > Research Affiliate, CSAIL, MIT > Phone: +1-617-724-5652 > Web : http://reuter.mit.edu > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_flatten error: bad vertex
Dear. Bruce. Thanks a lot for your help! I attached the tar.gz file for mri below. If you need anything more, let me know. Thanks, Ji Won replay06_mri.tar.gz <https://drive.google.com/file/d/0BxRUime4DPjvdGZjb1ZCOUFSNVU/view?usp=drive_web> 2016-03-17 11:40 GMT-04:00 Bruce Fischl : > Hi Ji > > that does sound strange! Can you tar and gzip the subject and upload it to > our website so I can see if I can replicate the problem? > > cheers > Bruce > > > On Thu, 17 Mar 2016, Ji Won Bang wrote: > > > Dear. Freesurfer experts. > > > > Hi. > > > > I'm having a problem with mris_flatten (version 5.3.0) > > > > > > Could you please help me fix this problem? > > > > My command line is: > > mris_flatten -w 0 -distances 12 7 > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d > > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat > > > > It returns the error: > > using write iterations = 0 > > sampling 7 neighbors out to a distance of 12 mm > > reading patch > /home/jbang/Projects/replay/mri//replay06/surf/lh.oc.patch.3d > > with 30434 vertices (20.5% of total) > > MRISreadPatch: bad vertex # (148517) found in patch file > > No such file or directory > > > > When making the patch lh.oc.patch.3d, I followed the processes below: > > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino > > -contrast UpperLower > > > > select 3 points along a boundary between upper and lower visual fields > (near > > calcarine sulcus) and press "Cut line". Then, select 4 points to define > the > > cutting plane: 1 on lower side of the line, 2 on upper side of the line, > 3 > > on the opposite surface (use rotation tool), and 4 to specify which > portion > > of surface is kept, and press "Cur plane". File->Patch->Save Patch As > > lh.oc.patch.3d > > > > So I think I made the patch correctly. > > > > ! weird thing that I suspect is that when I click save patch as, the > default > > location is $SUBJECTS_DIR/fsaverage/surf/ , so I had to change it to > > $SUBJECTS_DIR/$SUBJECT/surf > > > > Could you please help me? > > > > Thanks a lot! > > > > Best, > > Ji Won > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] mris_flatten error
Dear. Freesurfer experts. Hi. How are you? I'm trying to flatten the visual cortex using the command mris_flatten (freesurfer version 5.3.0). The command line is: mris_flatten -w 0 -distances 12 7 $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat The error I get is: using write iterations = 0 sampling 7 neighbors out to a distance of 12 mm reading patch /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with 27964 vertices (19.0% of total) MRISreadPatch: bad vertex # (147220) found in patch file No such file or directory Previously, Bruce advised me to recut it, so I deleted the lh.oc.patch.3d and recut it. However, freesurfer gives me the same error message... Could you please help me fix it? Thank you so much. Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_flatten error
Dear. Bruce. Thank you for your advice. I think I misunderstood what you meant. What I did is this. I showed the contrast result on a surface by using the command: tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino -contrast HorVer Then I cut line, and then plane (occipital plane) and save it(3d) as lh.oc.patch.3d under $SUBJECTS_DIR/$SUBJECT/surf/ I'm not sure if I regenerated the surface files correctly but I believe I created the surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process. Should I do something else to regenerate the surface? Thank you. Best, Ji Won 2016-03-22 11:39 GMT-04:00 Bruce Fischl : > what surface did you recut it from? Can you run mris_euler_number on that > surface (presumably the inflated) and also on the white/orig/pial > surfaces? They should all have the same number of vertices, but I suspect > some of them won't, meaning that they need to be regenerated. > > cheers > Bruce > > > > > On Tue, 22 Mar 2016, Ji Won Bang wrote: > > > Dear. Freesurfer experts. > > > > Hi. How are you? > > > > I'm trying to flatten the visual cortex using the command mris_flatten > (freesurfer > > version 5.3.0). > > > > The command line is: > > mris_flatten -w 0 -distances 12 7 > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d > > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat > > > > The error I get is: > > using write iterations = 0 > > sampling 7 neighbors out to a distance of 12 mm > > reading patch > /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with > > 27964 vertices (19.0% of total) > > MRISreadPatch: bad vertex # (147220) found in patch file > > No such file or directory > > > > Previously, Bruce advised me to recut it, so I deleted the > lh.oc.patch.3d and recut > > it. However, freesurfer gives me the same error message... > > > > Could you please help me fix it? > > > > Thank you so much. > > > > Best, > > Ji Won > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_flatten error
Dear. Bruce. Thanks for your help. When I tried: mris_euler_number rh.inflated.K It gave me: nquads=15728644, nvertices=574 ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices! Probably trying to use a scalar data file as a surface! When I tried: mris_euler_number lh.inflated It gave me: euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) When I tried: mris_euler_number rh.inflated It gave me: euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0 holes F =2V-4: 294364 = 294368-4 (0) 2E=3F:883092 = 883092 (0) So if everything is correct, I should see the same numbers for all surfaces, but since it's not the case, I should run recon again... Thanks, Ji Won 2016-03-22 12:24 GMT-04:00 Bruce Fischl : > you can try recon-all -make all for that subject and and see if it doesn > anything. But run mris_euler_number on those surfaces and see if they > match. They should all have the same number of faces/edges/vertices (for > one hemisphere in the same subject) > > On Tue, 22 Mar 2016, > Ji Won Bang wrote: > > > Dear. Bruce. > > > > Thank you for your advice. > > I think I misunderstood what you meant. > > > > What I did is this. > > I showed the contrast result on a surface by using the command: > > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino > -contrast HorVer > > > > Then I cut line, and then plane (occipital plane) and save it(3d) as > lh.oc.patch.3d > > under $SUBJECTS_DIR/$SUBJECT/surf/ > > > > I'm not sure if I regenerated the surface files correctly but I believe > I created the > > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all process. > > > > > > Should I do something else to regenerate the surface? > > > > Thank you. > > > > Best, > > Ji Won > > > > > > > > > > > > 2016-03-22 11:39 GMT-04:00 Bruce Fischl : > > what surface did you recut it from? Can you run mris_euler_number > on that > > surface (presumably the inflated) and also on the white/orig/pial > > surfaces? They should all have the same number of vertices, but I > suspect > > some of them won't, meaning that they need to be regenerated. > > > > cheers > > Bruce > > > > > > > > > > On Tue, 22 Mar 2016, Ji Won Bang wrote: > > > > > Dear. Freesurfer experts. > > > > > > Hi. How are you? > > > > > > I'm trying to flatten the visual cortex using the command > mris_flatten > > (freesurfer > > > version 5.3.0). > > > > > > The command line is: > > > mris_flatten -w 0 -distances 12 7 > > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.3d > > > $SUBJECTS_DIR/$SUBJECT/surf/lh.oc.patch.flat > > > > > > The error I get is: > > > using write iterations = 0 > > > sampling 7 neighbors out to a distance of 12 mm > > > reading patch > > /home/jbang/Projects/replay/mri//replay06/surf/rh.oc.patch.3d with > > > 27964 vertices (19.0% of total) > > > MRISreadPatch: bad vertex # (147220) found in patch file > > > No such file or directory > > > > > > Previously, Bruce advised me to recut it, so I deleted the > > lh.oc.patch.3d and recut > > > it. However, freesurfer gives me the same error message... > > > > > > Could you please help me fix it? > > > > > > Thank you so much. > > > > > > Best, > > > Ji Won > > > > > > > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > The information in this e-mail is intended only for the person to whom > it is > > addressed. If you believe this e-mail was sent to you in error and the > e-mail > > contains patient information, please contact the Partners Compliance > HelpLine > > at > > http://www.partners.org/complianceline . If the e-mail was sent to you > in error > > but does not contain patient information, please contact the sender and > > properly > > dispose of the e-mail. > > > > > > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mris_flatten error
Oh, I see. When I run all of these surfaces, it gave me the exactly same numbers... [jbang@cpu156 surf]$ mris_euler_number lh.inflated euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.white euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.pial euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.orig euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.sphere euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) total defect index = 0 [jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes F =2V-4: 289950 = 289954-4 (0) 2E=3F:869850 = 869850 (0) total defect index = 0 Thanks, Ji Won 2016-03-22 12:59 GMT-04:00 Bruce Fischl : > no, for all surfaces for the same hemi (lh and rh). lh.inflated.K is not a > surface - it's a scalar field over the surface. The ones that should be the > same are: > > lh.inflated > lh.white > lh.pial > lh.orig > lh.sphere > lh.sphere.reg > > > > and same for the rh (but different from the lh ones) > > > cheers > Bruce > > > On Tue, 22 Mar 2016, Ji Won Bang wrote: > > Dear. Bruce. >> >> Thanks for your help. >> >> When I tried: >> mris_euler_number rh.inflated.K >> >> It gave me: >> nquads=15728644, nvertices=574 >> ERROR: MRISread: file 'rh.inflated.K' has many more faces than vertices! >> Probably trying to use a scalar data file as a surface! >> >> When I tried: >> mris_euler_number lh.inflated >> >> It gave me: >> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes >> F =2V-4: 289950 = 289954-4 (0) >> 2E=3F:869850 = 869850 (0) >> >> When I tried: >> mris_euler_number rh.inflated >> >> It gave me: >> euler # = v-e+f = 2g-2: 147184 - 441546 + 294364 = 2 --> 0 holes >> F =2V-4: 294364 = 294368-4 (0) >> 2E=3F:883092 = 883092 (0) >> >> So if everything is correct, I should see the same numbers for all >> surfaces, but >> since it's not the case, I should run recon again... >> >> Thanks, >> Ji Won >> >> 2016-03-22 12:24 GMT-04:00 Bruce Fischl : >> you can try recon-all -make all for that subject and and see if it >> doesn >> anything. But run mris_euler_number on those surfaces and see if >> they >> match. They should all have the same number of faces/edges/vertices >> (for >> one hemisphere in the same subject) >> >> On Tue, 22 Mar 2016, >> Ji Won Bang wrote: >> >> > Dear. Bruce. >> > >> > Thank you for your advice. >> > I think I misunderstood what you meant. >> > >> > What I did is this. >> > I showed the contrast result on a surface by using the command: >> > tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis >> retino >> -contrast HorVer >> > >> > Then I cut line, and then plane (occipital plane) and save it(3d) >> as >> lh.oc.patch.3d >> > under $SUBJECTS_DIR/$SUBJECT/surf/ >> > >> > I'm not sure if I regenerated the surface files correctly but I >> believe >> I created the >> > surface($SUBJECTS_DIR/$SUBJECT/surf directory) from recon-all >> process. >> > >> > >> > Should I do something else to regenerate the surface? >> > >> > Thank you. >> > >> > Best, >> > Ji Won >> > >> > >> > >> > >> > >> > 2016-03-22 11:39 GMT-04:00 Bruce Fischl < >> fis...@nmr.mgh.harvard.edu>: >> > what surface
Re: [Freesurfer] mris_flatten error
Oh, I see.
I showed the contrast results on a surface using the command:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast UpperLower
Then I select 3 points along a boundary between upper and lower visual
fields (near calcarine sulcus) and press "Cut line". Then, select 4 points
to define the cutting plane: 1 on lower side of the line, 2 on upper side
of the line, 3 on the opposite surface (use rotation tool), and 4 to
specify which portion of surface is kept, and press "Cur plane".
File->Patch->Save Patch As {lh, rh}.oc.patch.3d
This is the usual way that I've been doing...
1 thing that's weird is when I run:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast UpperLower
It calls fsaverage..such as:
Reading source surface reg
/home/jbang/Projects/replay/mri//replay06/surf/lh.sphere.reg
Loading source data
Reading target surface reg
/home/jbang/Projects/replay/mri//fsaverage/surf/lh.sphere.reg
Done
Previously when everything went smooth, I think it did not call fsaverage.
Is it normal?
Thank you.
Best,
Ji Won
2016-03-22 13:06 GMT-04:00 Bruce Fischl :
> then you must not have cut the patch from those surfaces. The error is
> about a vertex # in the patch (147220), which is larger than the total
> number of vertices in those surfaces (144977), so it's out of bounds. How
> did you do the cutting?
>
>
> On Tue, 22 Mar 2016, Ji Won Bang wrote:
>
> Oh, I see.
>>
>> When I run all of these surfaces, it gave me the exactly same numbers...
>>
>> [jbang@cpu156 surf]$ mris_euler_number lh.inflated
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>> F =2V-4: 289950 = 289954-4 (0)
>> 2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.white
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>> F =2V-4: 289950 = 289954-4 (0)
>> 2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.pial
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>> F =2V-4: 289950 = 289954-4 (0)
>> 2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.orig
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>> F =2V-4: 289950 = 289954-4 (0)
>> 2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>> F =2V-4: 289950 = 289954-4 (0)
>> 2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>> F =2V-4: 289950 = 289954-4 (0)
>> 2E=3F:869850 = 869850 (0)
>>
>> total defect index = 0
>>
>> Thanks,
>> Ji Won
>>
>> 2016-03-22 12:59 GMT-04:00 Bruce Fischl :
>> no, for all surfaces for the same hemi (lh and rh). lh.inflated.K
>> is not
>> a surface - it's a scalar field over the surface. The ones that
>> should be
>> the same are:
>>
>> lh.inflated
>> lh.white
>> lh.pial
>> lh.orig
>> lh.sphere
>> lh.sphere.reg
>>
>>
>>
>> and same for the rh (but different from the lh ones)
>>
>> cheers
>> Bruce
>>
>>
>> On Tue, 22 Mar 2016, Ji Won Bang wrote:
>>
>> Dear. Bruce.
>>
>> Thanks for your help.
>>
>> When I tried:
>> mris_euler_number rh.inflated.K
>>
>> It gave me:
>> nquads=15728644, nvertices=574
>> ERROR: MRISread: file 'rh.inflated.K' has many more faces
>> than vertices!
>> Probably trying to use a scalar data file as a surface!
>>
>> When I tried:
>> mris_euler_number lh.inflated
>>
>> It gave me:
>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0
>> holes
>> F =2V-4: 289950 = 289954-4 (0)
>> 2E=3F:869850 = 869850 (0)
>>
>> When I tried:
>> mris_euler_number rh.inflated
>>
Re: [Freesurfer] mris_flatten error
Dear. All.
I tried tksurfer and it works.. It's still very strange why tksurfer-sess
does not work.
The command line that worked successfully is:
tksurfer replay06 lh inflated -curv -gray
Then I overlayed the contrast result sig.nii.gz and the registration file.
Then I cut the plane and then flattenr the cortex.
The command that did not work well is:
tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
-contrast UpperLower
For some reason, it calls fsaverage map and when I cut the plane, it seems
like the vertex is off the surface that I created... Probably, this cutting
work was done in other surface that I did not intend...
If anyone knows why it's happening, let me know.
Thank you!
Best,
Ji Won
2016-03-22 13:18 GMT-04:00 Ji Won Bang :
> Oh, I see.
>
> I showed the contrast results on a surface using the command:
> tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
> -contrast UpperLower
>
> Then I select 3 points along a boundary between upper and lower visual
> fields (near calcarine sulcus) and press "Cut line". Then, select 4 points
> to define the cutting plane: 1 on lower side of the line, 2 on upper side
> of the line, 3 on the opposite surface (use rotation tool), and 4 to
> specify which portion of surface is kept, and press "Cur plane".
> File->Patch->Save Patch As {lh, rh}.oc.patch.3d
>
> This is the usual way that I've been doing...
>
> 1 thing that's weird is when I run:
> tksurfer-sess -s $SUBJECT -df sessdirfile -hemi lh -analysis retino
> -contrast UpperLower
> It calls fsaverage..such as:
> Reading source surface reg
> /home/jbang/Projects/replay/mri//replay06/surf/lh.sphere.reg
> Loading source data
> Reading target surface reg
> /home/jbang/Projects/replay/mri//fsaverage/surf/lh.sphere.reg
> Done
>
> Previously when everything went smooth, I think it did not call fsaverage.
>
> Is it normal?
>
> Thank you.
>
> Best,
> Ji Won
>
>
>
> 2016-03-22 13:06 GMT-04:00 Bruce Fischl :
>
>> then you must not have cut the patch from those surfaces. The error is
>> about a vertex # in the patch (147220), which is larger than the total
>> number of vertices in those surfaces (144977), so it's out of bounds. How
>> did you do the cutting?
>>
>>
>> On Tue, 22 Mar 2016, Ji Won Bang wrote:
>>
>> Oh, I see.
>>>
>>> When I run all of these surfaces, it gave me the exactly same numbers...
>>>
>>> [jbang@cpu156 surf]$ mris_euler_number lh.inflated
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>> F =2V-4: 289950 = 289954-4 (0)
>>> 2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.white
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>> F =2V-4: 289950 = 289954-4 (0)
>>> 2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.pial
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>> F =2V-4: 289950 = 289954-4 (0)
>>> 2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.orig
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>> F =2V-4: 289950 = 289954-4 (0)
>>> 2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>> F =2V-4: 289950 = 289954-4 (0)
>>> 2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>> [jbang@cpu156 surf]$ mris_euler_number lh.sphere.reg
>>> euler # = v-e+f = 2g-2: 144977 - 434925 + 289950 = 2 --> 0 holes
>>> F =2V-4: 289950 = 289954-4 (0)
>>> 2E=3F:869850 = 869850 (0)
>>>
>>> total defect index = 0
>>>
>>> Thanks,
>>> Ji Won
>>>
>>> 2016-03-22 12:59 GMT-04:00 Bruce Fischl :
>>> no, for all surfaces for the same hemi (lh and rh). lh.inflated.K
>>> is not
>>> a surface - it's a scalar field over the surface. The ones that
>>> should be
>>> the same are:
>>>
>>> lh.inflated
>>> lh.white
>>> lh.pial
>>> lh.orig
>>
[Freesurfer] mri_label2vol check-up
Dear. Freesurfer experts. Hi. How are you? I'd appreciate it a lot if you can help me with this problem. I'm trying to check the ROI (.nii) after creating it by using mri_label2vol command. I used the command: mri_label2vol --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1vt.label --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1dt.label --temp $DATA_DIR/$SUBJECT/bold_retino/025/fmcpr.nii.gz --reg $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat --o $DATA_DIR/$SUBJECT/roimask/test.nii tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay $DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01 However, this tkmedit command looks for test.dat file instead of test.nii and does not show ROI. Could you please tell me what's going wrong? Thank you! Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] mri_label2vol check-up
Dear. Experts. Please ignore the previous email. It works. Thank you. Best, Ji Won 2016-03-23 17:24 GMT-04:00 Ji Won Bang : > Dear. Freesurfer experts. > > Hi. How are you? > > I'd appreciate it a lot if you can help me with this problem. > > I'm trying to check the ROI (.nii) after creating it by using > mri_label2vol command. > > I used the command: > > mri_label2vol --label $SUBJECTS_DIR/$SUBJECT/label/lh.v1vt.label --label > $SUBJECTS_DIR/$SUBJECT/label/lh.v1dt.label --temp > $DATA_DIR/$SUBJECT/bold_retino/025/fmcpr.nii.gz --reg > $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat --o > $DATA_DIR/$SUBJECT/roimask/test.nii > > tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay > $DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg > $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01 > > However, this tkmedit command looks for test.dat file instead of test.nii > and does not show ROI. > > Could you please tell me what's going wrong? > > Thank you! > > Best, > Ji Won > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] ROI within subject
Dear. Freesurfer experts. Hi. How are you? I have a question about making ROI. This might be a naive question, but any input would be greatly appreciated. I preprocessed scans per run, thus I have register.dof6.dat file inside all run epi directories. Then, I made ROIs per single subject based on the single subject's functional contrast map using the command: tksurfer replay06 lh inflated -curv -gray I overlayed the single subject's contrast result sig.nii.gz (obtained from 3 runs) and the registration file in 1 run(register.dof6.dat in 1 among 3 runs), then I cut the plane and then flattenr the cortex, made ROI. While trying to check the ROIs, I realized that this ROI seems to be slightly different depending on which register.dof6.dat I use (I tried all 3 runs' register.dof6.dat when overlaying). tkmedit -f $SUBJECTS_DIR/$SUBJECT/mri/norm.mgz -overlay $DATA_DIR/$SUBJECT/roimask/test.nii -overlay-reg $DATA_DIR/$SUBJECT/bold_retino/025/register.dof6.dat -fthresh 0.01 I thought ideally, this functional ROI should be the same across all runs if thes register files are perfectly registering each functional sans to anatomical scan. Is this a usual way when people make ROI based on functional contrast map per each subject? The way I did in the past did not have this kind of problem because I did motion correction as targetting the first EPI (aligning all images to the first EPI) and then used only 1 (same) register.dat file.. Please share your idea with me. Thank you very much. Best, Ji Won ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] question regarding creating Brodmann area
Dear. freesurfer users. I'm trying to make a label for Brodmann area 44. According to the freesurfer manual, I've run, recon-all -s subjid -ba-labels However, it says Flag -ba-labels unrecognized. I'm using freesurfer version 4.5.0. By default, recon-all is supposed to create Brodmann areas under label directory. However, inside the lable directory, I see only aparc.annot.a2009s.ctab aparc.annot.ctab lh.aparc.a2009s.annot lh.aparc.annot lh.cortex.label rh.aparc.a2009s.annot rh.aparc.annot rh.cortex.label Please leave me any comment!! I appreciate it a lot! Best regards, Ji Won Bang ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] resolution/size mismatch when extracting BOLD from subfields of hippocampus
Dear Freesurfer experts,
I'd appreciate any of your comments a lot!
I'm trying to extract BOLD signals from subfields of hippocampus but
somehow I find resolution/size mismatch such that the assigned voxel number
of subfield hippocampus is greater than voxel numbers of whole brain BOLD
data.
I initially processed data using freesurfer version 5.3.0. but then
recently created subfields of hippocampus using version 6.0 due to
reviewer's request for additional analysis for hippocampus.
Below are the steps that I tried.
(1) creating subfields of hippocampus
recon-all -s subjectID -hippocampal-subfileds-T1
mri_extract_label lh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 leftCA1.mgz
mri_extract_label rh.hippoSfLabels-T1.v10.FSvoxelSpace.mgz 206 rightCA1.mgz
mris_calc -o CA1.mgz leftCA1.mgz add rightCA1.mgz
mri_convert CA1.mgz CA1.nii.gz
mri_convert CA1.nii.gz $DATA_DIR/$SUBJECT/roimask/CA1.nii
(2) extracting BOLD from subfield ROI using matlab code
% get roi mask
roi = MRIread([homeDir epiDir subject '/' roiDir rois{ROI} '.nii']);
roimask = find(fast_vol2mat(roi)>0);
Nvoxel = length(roimask);
% loading BOLD data from run
data = [];
for RUN = 1
% read data from motion-corrected data
f = MRIread([homeDir spider subject '/' boldDir dirs(RUN).name '/'
boldFile '.nii']);
fmat = fast_vol2mat(f);
[numTR numVoxelAll] = size(fmat);
data(:,:,:,RUN) = fmat(:,roimask)';
end
Below is the error:
Nvoxel(length of roimask) for CA1 is 1385 and for example, roimask(1) is
7576977 meaning that its voxel number is assigned to 7576977.
Then size(fmat) = 150 175232.
So fmat(:, roimask(1)) which is again fmat(:, 7576977) gives me an error
that index exceeds matrix dimensions
Why does it happen?
Please help me extract the BOLD signals from subfields of hippocampus!
Thanks for your help in advance.
Best,
Ji Won
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
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