[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

[Freesurfer] unpacking error

e]; }" (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 Fre

Re: [Freesurfer] unpacking error

h 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: >

Re: [Freesurfer] unpacking error

/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_D

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:

[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 t

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 dcm

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,

[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/bol

Re: [Freesurfer] error in motion correction

tino) 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. > >

Re: [Freesurfer] error in motion correction

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 sl

Re: [Freesurfer] error in motion correction

unctional 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 argu

[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 t

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

Re: [Freesurfer] error in mc-sess

-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: &

[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 in

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

Re: [Freesurfer] mkbrainmask-sess and inorm-sess

rm 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:

[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

Re: [Freesurfer] [freesurfer] selxavg-sess question

ing ==> 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); >> -

[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 err

Re: [Freesurfer] selxavg3-sess question

ought 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. > &g

[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 ar

[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).

Re: [Freesurfer] mri_robust_register question

tered 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 t

[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: u

[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

Re: [Freesurfer] mri_robust_register question

o 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. > >> > >

Re: [Freesurfer] mris_flatten error: bad vertex

> 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. > > >

[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

Re: [Freesurfer] mris_flatten error

> 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

Re: [Freesurfer] mris_flatten error

> 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 Ma

Re: [Freesurfer] mris_flatten error

e > 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.in

Re: [Freesurfer] mris_flatten error

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: > &g

Re: [Freesurfer] mris_flatten error

tting 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 $S

[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_D

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 chec

[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

[Freesurfer] question regarding creating Brodmann area

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

[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 i