Freesurfer

freesurfer@nmr.mgh.harvard.edu

17 participants
30099 discussions

Re: [Freesurfer] trac-all inquiry
by David Soto 17 Dec '13

17 Dec '13

thanks Anastasia, see the link below pls https://dl.dropboxusercontent.com/u/8209026/regs.zip you will find 2 pairs of images pair one: there are 2 files starting by ind2anat, one showing the T1 and the other the FA in the same coordinates, you will see that align well pair two: here are 2 files starting by MNI, one showing the FA in mni space and the other the mni T1_1mm template..seem fine to me, though there seem to be some coverage deficit in the FA map in the bottom right of the image cheers ds On Mon, Dec 2, 2013 at 8:16 PM, Anastasia Yendiki < ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi David - I am not convinced that all the regisrtrations have worked well > for this subject. The fact that some of the coordinates of the control > points, which are mapped from template to individual space, are negative > in individual space (see INFO messages in log file), means that some part > of the brain in templated space is mapped outside the field of view in > individual DWI space. Can you send any screenshots that show the quality > of the DWI to anatomical and DWI to MNI registrations? > > Thanks, > a.y > > On Mon, 2 Dec 2013, David Soto wrote: > > > hi - thanks , not sure though...the no_dif brain maskseems ok, if that is > > what you meant... > > > > I did re-run the processing and > > in the last run I can not see the WARN you mentioned > > the latest preprocessing output from the preprocessing can be > > found here: https://dl.dropboxusercontent.com/u/8209026/prepro.txt > > > > the dlabel/diff output got stuck with the > > rh.ilf_AS_avg33 which only contains thee _mni_bbr_cpts_5.txt but nothing > > else > > > > thanks so much > > > > ds > > > > > > > > On Mon, Dec 2, 2013 at 10:59 AM, Anastasia Yendiki > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > Hi David - Sorry for the delayed response due to traveling. > > > > There's a warning about the right ILF in the log file that may > > offer a > > clue: > > > > WARN: Initial control point 37 56 -6 is not in DWI volume - is > > DWI cropped? > > WARN: Replacing with closest point in volume (37 56 0) > > WARN: Initial control point 38 45 -1 is not in DWI volume - is > > DWI cropped? > > WARN: Replacing with closest point in volume (38 45 0) > > WARN: Initial start point 37 56 0 is not in start ROI > > WARN: Replacing with closest point in start ROI (31 56 0) > > > > Is the brain mask cropped on either end of the right ILF? You > > mentioned > > that you already checked the registration of the FA map to the > > template > > space (dmri/mni/dtifit_FA.bbr.nii.gz), so I'm assuming there's > > nothing > > wrong there. > > > > a.y > > > > On Sat, 16 Nov 2013, David Soto wrote: > > > > > Thanks! > > > for some weird unknown reason > > > the log for the preprocessing file of this > > > subject is unusually big (2.8 megabytes) > > > please get it from this link > > > https://dl.dropboxusercontent.com/u/8209026/Archive.zip > > > cheers > > > ds > > > > > > > > > On Sat, Nov 16, 2013 at 3:13 PM, Anastasia Yendiki > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > Hi David - This log only shows output from the -path > > step and > > > not from the -prep step. The file that's missing should > > be > > > created during the -prep step, so there's no way to > > figure out > > > what went wrong without seeing the output from the > > > pre-processing. > > > > > > Please cc the freesurfer list on your reply. > > > > > > Thank you, > > > a.y > > > > > > > > > On Sat, 16 Nov 2013, David Soto wrote: > > > > > > Thanks, please see attachedI only noticed this > > > ERROR: > Couldnotopen/home/dsoto/Documents/fmri/rsdtianawmgui/14AB/dlabel/diff/rh.ilf_AS_ > > avg > > > 33_m > > > ni_bbr_cpts_5_std.txt > > > cheers > > > DS > > > > > > > > > On Fri, Nov 15, 2013 at 8:55 PM, Anastasia Yendiki > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > Hi David - Can you please send us the > > > trac-all.log file for this > > > subject? > > > Without seeing where it stopped and what > > error > > > messages there > > > are it's > > > hard to guess what's going on. > > > > > > Thanks, > > > a.y > > > > > > On Fri, 15 Nov 2013, David Soto wrote: > > > > > > > Hi - > > > > trac-all completed in all my Ps except one > > > > and I noticed that the dlabel/diff output > > > does not contain > > > all the files > > > > > > > > I assessed whether it could be do to poor > > > registration, by > > > checking > > > > the aparc+aseg > > > > file and looks allright > > > > > > > > I also checked the registration of FA maps > > > to standard space > > > by > > > > freeview -v > > > $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz > > > > dtifit_FA.bbr.nii.gz > > > > and seems fine > > > > > > > > also > > > > > > > > freeview -v brain_anat_orig.nii.gz > > > lowb_brain.nii.gz > > > > > > > > which also seems fine > > > > > > > > any ideas pls? > > > > > > > > thanks! > > > > > > > > ds > > > > > > > > > > > > > > > > On Fri, Aug 16, 2013 at 5:14 PM, Anastasia > > > Yendiki > > > > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > > > > > > > I suspect the current problem is > > > caused by poor > > > registration. > > > > Have you checked the aparc+aseg > > and/or > > > the registration > > > from > > > > diffusion to anatomical and from > > > anatomical to MNI? > > > > > > > > On Fri, 16 Aug 2013, David Soto > > > wrote: > > > > > > > > > > > > > > > > -- > > > > > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > > > > > > > > > > > > > > > > > > > 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. > > > > > > > > > > > > > > > -- > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > -- > > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > > > > > > > > > > > > > > > -- > > http://www1.imperial.ac.uk/medicine/people/d.soto/ > > > > > -- http://www1.imperial.ac.uk/medicine/people/d.soto/

2 10

talairach transformation error and general recon-all error
by JARED NIELSEN 17 Dec '13

17 Dec '13

Hi, I'm new to FreeSurfer and have been going through the tutorials, YouTube videos, and Mail Archive. I've run recon-all on a handful of scans with variable success. Some of the scans are processed after five or six hours without any problems, and the output looks good. Others are processed "without any errors" after a matter of minutes, and logically I don't see any output. Finally, others hit a hard error after a few minutes of processing during the talairach transformation step. I looked at the orig.mgz file (for the scan that failed at transformation step) through tkmedit, and it is a blank white rectangle. I don't see anything that resembles a head or brain. I've attached examples of each recon-all.log (i.e., good, bad, and bad_talairach). Any help would be greatly appreciated. Thanks, Jared

3 4

GLM p value display
by Celine Louapre 17 Dec '13

17 Dec '13

Hi all I am wondering what is the best to present GLM results in a table on top of the visual display. For the significant clusters after clusterwise correction, should we display the Max -log10(p) as in the summary file itself, or the p value directly, or a transformed pvalue like a Z score? Thanks for advices Celine -- Celine Louapre, MD Research Fellow at Massachusetts General Hospital Department of Radiology, MGH Building 149, Room 2301 13th Street Charlestown, MA 02129

2 3

mri_glmfit-sim Error
by Jon Wieser 17 Dec '13

17 Dec '13

After running a group comparison using qdec I wanted to use mc-z for multiple comparison correction I tried running: mri_glmfit-sim \ --glmdir MTA_ADHD_MJ2 \ --sim mc-z 1000 2.0 mc-z.negative \ --sim-sign abs --cwpvalthresh 0.999 \ --overwrite ERROR: dimension mismatch between X and contrast MTA_ADHD_MJ2/tmp.mri_glmfit-sim-9440/lh-Avg-thickness-Age-Cor.mtx X has 4 cols, C has 8 cols What does this mean and how to fix it? -- Jon Wieser Research Specialist UW-Milwaukee Psychology Department, Pearse Hall Rm 366 2441 East Hartford Ave Milwaukee, WI 53211 Phone: 414-229-7145 Fax: 414-229-5219

1 0

Tracula upgrading to Freesurfer 5.3
by Laura Christine Anderson 17 Dec '13

17 Dec '13

Tracula experts, I was hoping to upgrade to Freesurfer 5.3 in order to use the new motion detection feature of Tracula. The issue is that all of the preprocessing has already been completed in Freesurfer 5.2 with the older version of Tracula. Would I need to redo all the preprocessing in 5.3 in order to use the new motion detection feature? Thanks for your help! Laura Laura C. Anderson, B.A. Graduate Student Clinical & Developmental Psychology University of Maryland College Park, MD 20742 BPS 0112

1 0

data uploaded
by Rujing Zha 17 Dec '13

17 Dec '13

Hi Bruce, I uploaded the data to your server. All files can be divided into 2 subjects. And one subject has incorrect segmentation (subject), the other has a multiframe ERROR(LJH_error). Thanks. All the best. 2013-12-17 Rujing Zha

2 1

Very strange error in surface reconstruction after a2-cp
by Paola Valsasina 17 Dec '13

17 Dec '13

Dear FS experts, I have a very strange error after running autorecon2-cp. I never saw this kind of error with previous versions of FS. I run recon-all -all on my subject, and obtained very good surface reconstructions, with the exception of few excluded wm voxels (see attachment called "before autorecon2-cp"). I added few control points throughout the entire image (for a total of 20 control points) and I run -autorecon2-cp -autorecon3 on the same subject. The output I obtain is very bad (see attachment called "after autorecon2-cp"). How is it possible that adding 20 control points causes such a surface distortions?!! I never had this error with previous FS versions. Thank you for any suggestion. Kind regards, Paola

1 0

Optimal registration
by Dídac Vidal 17 Dec '13

17 Dec '13

Hi, I'd like to ask whether there exist any (implemented/objective) measure to identify a correct surface reconstruction beyond the visual inspection in order to identify gross defect or wm/gm boundary. Thanks in advance. -- Dídac Vidal Piñeiro Dept. Psychiatry and Clinical Psychobiology Faculty of Medicine University of barcelona

2 1

Fw: Re: unpacksdcmdir: specifies unpacking rules from the command-line ERROR
by Rujing Zha 16 Dec '13

16 Dec '13

Hi Bruce, Thanks Bruce. Would you please help me deal with another two problems? The 1st one is : There is a excellent segmentation in -surfs after editing the pial and running -autorecon-pial. Some voxels was removed from the brainmask.mgz in editing the pial. However the -aseg image still have those voxels which I have removed from the brainmask.mgz. Does this aseg image will influence my group thickness analysis if I donot process additionally? There are brainmask.mgz(pic 1) and aseg(pic 2) snapshots in the attachment. The 2nd one is : I could not visualize the inflated image properly by tksurfer. Here was the detailed describe: tksurfer yizhihui rh inflated I could see little thing in the tksurfer after typing the command above. The result can be got in picture 3 of the attachment and the standard output message can be seen in the picture 4. I had visualized it in the freeview tool by typing "freeview -f $SUBJETCS_DIR/yizhihui/surf/rh.inflated ". The result can be seen in picture 5. CentOS 5.8 is used in my server and I use "freesurfer-Linux-centos4-stable-pib-v5.3.0". Thanks in advance. All the best. 2013-12-17 Rujing Zha School of Life Science University of Science and Technology of China E-mail: zharj(a)mail.ustc.edu.cn charujing(a)gmail.com charujing123(a)163.com 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> 发送时间：2013-12-16 23:57 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the command-line ERROR 收件人："Rujing Zha"<charujing123(a)163.com> 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> Hi Rujing you can use either our FTP site or our file drop. Info for this is at http://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange and https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html cheers Bruce On Mon, 16 Dec 2013, Rujing Zha wrote: > Hi Bruce, > Maybe 163 email has some problems. I will try my gmail to send you and Louis > my data. But I donot know whether your email can get attachment size 289M? > Thanks. > All the best. > > 2013-12-16 > > ____________________________________________________________________________ > Rujing Zha > > ____________________________________________________________________________ > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > 发送时间：2013-12-16 22:37 > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the > command-line ERROR > 收件人："Rujing Zha"<charujing123(a)163.com> > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > no, I didn't get it > On Mon, 16 Dec 2013, Rujing Zha wrote: > > > Dear Bruce, > > Thanks Bruce. That's all right. > > I want to know if I e-mail to you my subject's data successfully. The > > subject's image had a incorrect segmentation in surfs after recon-all. > > Thanks in advance. > > All the best. > > > > 2013-12-16 > > > > _________________________________________________________________________ > ___ > > Rujing Zha > > > > _________________________________________________________________________ > ___ > > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > 发送时间：2013-12-16 22:24 > > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from the ?? ?> command-line ERROR > > 收件人："Rujing Zha"<charujing123(a)163.com> > > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > > > sorry, I don't know that code very well. Doug is probably the right one t > o > ?? ? > > help you > > Bruce > > > > > > On Mon, 16 Dec 2013, Rujing Zha wrote: > > > > > Dear Bruce, > > > I did setup the "-run 015" not "013" in unpacksdcmdir as I told in prev > io > > us > > > message. But it generated the "013" folder automatically after running ?? ? > > > unpacksdcdir, which made me so confused. > > > As it created the "013" folder, I guess unpacksdcmdir didnot recognized > > > > structure image correctly which was in the "15th" line of the scan.info > . > ?? ?> Thanks Bruce. > > > All the best. > > > > > > 2013-12-16 > > > > > > _______________________________________________________________________ > __ > > ___ > > > Rujing Zha > > > > > > _______________________________________________________________________ > __ > > ___ > > > 发件人：Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > > > 发送时间：2013-12-16 22:12 > > > 主题：Re: [Freesurfer] unpacksdcmdir: specifies unpacking rules from th > e > ?? ?> command-line ERROR > > > 收件人："Rujing Zha"<charujing123(a)163.com> > > > 抄送："freesurfer"<freesurfer(a)nmr.mgh.harvard.edu> > > > > > > but why are you giving recon-all the path to run 013 instead of 015? I ?? ? > ?? ?> don't know the fsfast file structure, but your scan.info says that 01 > 3 is > > > > ?? ?an EPI fun and 015 is the mprage > > > > > > On Sat, > > > 14 Dec 2013, Rujing Zha wrote: > > > > > > > Hi Bruce, > > > > It generated a 013 subfolder in after running this code "unpacksdcmdi > r > ?? ? > > > > -src ../data/liujunhao -targ ../work/liujunhao -fsfast -run 015 3dana > t > ?? ?mg > > > z > > > > 001.mgz". It is 15 that I can see the number of t1_mpr_ns_sag_iso_zh > an > > g > > ?? ?in > > > > the unpack.log. > > > > Then I ran "recon-all -i ../work/liujunhao/3danat/013/001.mgz -s liuj > un > > ha > > > o", > > > > and it finished without error. > > > > "recon-all -s liujunhao -all" was run and ERROR would be displayed: ?? ? > > > > ERROR: input(s) cannot have multiple frames! > > > > The recon-all.log unpack.log and scan.info were unloaded in the attac > hm > > en > > > t. > > > > Thanks. > > > > All the best. > > > > > > > > 2013-12-14 > > > > > > > > _____________________________________________________________________ > __ > > __ > > > ___ > > > > Rujing Zha > > > > > > > > > > > _______________________________________________ > > > Freesurfer mailing list > > > Freesurfer(a)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 > > i > > > s > > > addressed. If you believe this e-mail was sent to you in error and the ?? ?e- > > ma > > > il > > > contains patient information, please contact the Partners Compliance He > lp > > Li > > > ne at > > > http://www.partners.org/complianceline . If the e-mail was sent to you ?? ?in > > e > > > rror > > > but does not contain patient information, please contact the sender and > p > > ro > > > perly > > > dispose of the e-mail. > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 i > s > addressed. If you believe this e-mail was sent to you in error and the e-ma > il > contains patient information, please contact the Partners Compliance HelpLi > ne at > http://www.partners.org/complianceline . If the e-mail was sent to you in e > rror > but does not contain patient information, please contact the sender and pro > perly > dispose of the e-mail. > > >

1 0

Re: [Freesurfer] problem creating annotation using mri_sample_parc?
by Markus Gschwind 16 Dec '13

16 Dec '13

Dear Bruce or someone else, would you mind answering a little more in detail, please? I am stuck. There is hardly any thread about the command mris_sample_parc, but I need this function. 1) This file called "cma_parcellation_colors.txt", is an option for mris_sample_parc. Where does that file come from? How am I supposed to create it? 2) What is missing if the loading of the created annotation file onto a surface (in freeview) gives the following error, repeating for infinity CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory CTABfindAnnotation: ct was NULL No such file or directory What does this error mean, at all? Thank you and please excuse my insisting! Markus 2013/12/14 Markus Gschwind <markus.gschwind(a)gmail.com> > Thank you Bruce, > > I read that mris_sample_parc "samples a volumetric parcellation onto a > surface". > > I understand that this is like creating from a file of the type of aseg a > corresponding file of the type of aparc.annot.ctab. > > Is this not true? Do I actually have to create the aparc.annot.ctab type > file manually and give this as the above mentionned file to the command? > The file is only an optional arguement though? > > Thanks again, Markus > > > 2013/12/14 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > >> Hi Markus >> >> you need to create that file (or update FreeSurferColorLUT.txt) to >> reflect whatever you have in /Documents/myROIfile.mgz >> >> cheers >> Bruce >> >> >> On Sat, 14 Dec 2013, Markus Gschwind wrote: >> >> Dear Bruce, >>> Thank you for your answer. I have not yet gotten it correctly. >>> >>> 1) Where does that file come from? Should I create it? how? >>> >>> 2) what is missing in the command of mris_sample_parc? Why does it now >>> work? >>> >>> 3) what does the second error mean? >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> >>> Thanks in advance! >>> [cleardot.gif] >>> >>> Markus >>> >>> >>> 2013/12/13 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >>> Hi Markus >>> >>> that file translates indices/annotations into colors to display >>> and human reasable names. >>> >>> cheers >>> Bruce >>> On Fri, 13 Dec 2013, Markus Gschwind wrote: >>> >>> I can precise the question, actually there are >>> three: >>> >>> 1) ist the command correct? >>> >>> mris_sample_parc -v -sdir subject001 rh >>> ~/Documents/myROIfile.mgz rh.myROIfile.annot >>> >>> >>> 2) I do not understand the meaning of this claimed >>> file >>> cma_parcellation_colors.txt >>> >>> Actually this does not exist. In the Wiki >>> (http://surfer.nmr.mgh.harvard.edu/fswiki/mris_sample_parc) >>> it says that >>> there was an optional arguement >>> >>> -file <filename> >>> >>> use <filename> as translation (default: >>> 'cma_parcellation_colors.txt') >>> >>> >>> If I understand correctly, "translation" points ot a >>> problem of different >>> spaces, but the filename rather seems something like >>> a parcellation/atlas >>> color table? >>> >>> 3) The result of this problem seems to be that I >>> cannot annotate the surface >>> using the created annotation file. It gives this >>> error, which i do not >>> understand. >>> >>> >>> >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> CTABfindAnnotation: ct was NULL >>> No such file or directory >>> ... etc. >>> >>> Can anyone help me find the problem? >>> >>> >>> Thank you in advance! >>> >>> Markus >>> >>> >>> >>> >>> 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. >>> >>> >>> >>> >

2 1

Jump to page:

2026

2025

2024

2023

2022

2021

2020

2019

2018

2017

2016

2015

2014

2013

2012

2011

2010

2009

2008

2007

2006

2005

2004

Freesurfer