Freesurfer November 2015

freesurfer@nmr.mgh.harvard.edu

138 participants
239 discussions

Extract single time frame
by Rockers, Elijah D. 16 Oct '22

16 Oct '22

Hello again, I have a large time series in dicom or .nii format. I am interested in extracting a single time frame from it. I did this before, I believe with freesurfer, but I have somehow forgot the name of the command, and I can't seem to find it. I believe it could be used to specify particular regions of the volume, as well as time. I need the entire volume, still, but only one frame. Thanks in advance! Eli Houston Methodist. Leading Medicine. Ranked by U.S.News & World Report as one of America's "Best Hospitals" in 11 specialties. Named to FORTUNE® Magazine's "100 Best Companies to Work For®" list 10 years in a row. Designated as a Magnet hospital for excellence in nursing. Visit us at houstonmethodist.org. Follow us at twitter.com/MethodistHosp and www.facebook.com/HoustonMethodist. ***CONFIDENTIALITY NOTICE*** This e-mail is the property of Houston Methodist Hospital and/or its relevant affiliates and may contain restricted and privileged material for the sole use of the intended recipient(s). Any review, use, distribution or disclosure by others is strictly prohibited. If you are not the intended recipient (or authorized to receive for the recipient), please contact the sender and delete all copies of the message. Thank you.

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Re: [Freesurfer] [tracula] error running trac-all -prep
by Borsodi Florian 20 Dec '17

20 Dec '17

Hi Anastasia, Yes, i am running this on ubuntu 12.04. Sincerely, Florian >>> Anastasia Yendiki 20.08.13 17.38 Uhr >>> Hi Florian - Are you running this on an ubuntu system by any chance? a.y On Tue, 20 Aug 2013, Borsodi Florian wrote: > Hi Anastasia, > > Thank you for your help. > I changed the commas in "/dmri/bvecs" to dots and reran trac-all. But the command "xfmrot" changed the dots back to > commas. So, I changed our system language from de_AUT.UTF-8 to en_US.UTF-8 and reran trac-all. After changing the > system language everything was genereted correctly and trac-all -prep ran without any errors. > I'm so glad. > > Then, I started the next step "trac-all -bedp" and got a syntax error "/usr/local/freesurfer/bin/bedpostx_mgh: 131: > /usr/local/freesurfer/bin/bedpostx_mgh: Syntax error: "(" unexpected. " I also attached the the logfile. I was reading > about this error in the mail archive. Would I have to run "bedpostx" outside of tracula ? > > Sincerely, > Florian > > >>> Anastasia Yendiki 19.08.13 17.54 Uhr >>> > > Hi Florian - Can you please change the decimal commas to points and try > again? > > a.y > > On Mon, 19 Aug 2013, Borsodi Florian wrote: > > > Hi Anastasia, > > > > Here are the bvec and bval files you asked me about. > > > > Sincerely, > > Florian > > > > >>> Anastasia Yendiki 18.08.13 22.52 Uhr >>> > > > > Hi Florian - Can you please also attach the bvecs/bvals files from the > > dmri directory? > > > > Thanks, > > a.y > > > > On Sun, 18 Aug 2013, Borsodi Florian wrote: > > > > > Hi Anastasia, > > > > > > Thanks for your help. I renamed the directories and reran trac-all. It > > > worked for the moment. > > > However, then I got another error: "bvecs and bvals don't have the same > > > number of entries." > > > I don't know why, because they actually have the same number of entries. > > > > > > I attached the logfile so that you may see what is going on. The error > > > occours at line 1463. > > > > > > Thank you in advance for your help. > > > > > > Sincerely, > > > Florian > > > > > > > > > >>> Anastasia Yendiki 15.08.13 18.01 Uhr >>> > > > > > > Hi Florian - I see what's going on. Can you please rename the directory > > > /data/physics/florian/nii into something that doesn't include "nii", and > > > rerun? Because "nii" is a file extension, this confuses some of the > > > scripts. > > > > > > Thanks, > > > a.y > > > > > > On Thu, 15 Aug 2013, Borsodi Florian wrote: > > > > > > > Hi Anastasia > > > > > > > > I ran the command you sent me and it runs without any errors. > > > > I also attached the command line for you. > > > > > > > > Furthermore i ran data with 12 diffusion directions and i keep getting the > > > > same kind of problems. > > > > > > > > sincerely > > > > Florian > > > > > > > > >>> Anastasia Yendiki 02.08.13 19.59 Uhr > > > >>> > > > > > > > > Hi Florian - Can you please run this command directly on the command line > > > > and see if there are any errors? > > > > > > > > flip4fsl > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.nii.gz > > > > /data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig_flip.nii.gz > > > > > > > > Thanks, > > > > a.y > > > > > > > > On Fri, 2 Aug 2013, Borsodi Florian wrote: > > > > > > > > > Hi Anastasia > > > > > > > > > > Thank you for your answer. > > > > > > > > > > Yes, those files exist. > > > > > I also extracted the bvec an bval files with anotther software then > > > > dcm2nii > > > > > and i keep getting the same kind of error. > > > > > Also, about the 6 diffusion direction, those data i sent you, are just > > > > > testdata for running tracula. > > > > > > > > > > sincerely > > > > > Florian > > > > > > > > > > >>> Anastasia Yendiki 02.08.13 0.41 Uhr > > > >>> > > > > > > > > > > Hi Florian - Do these files exist? > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bvec > > > s > > > > > > > > > > > > >>/data/physics/florian/nii/1020000485074_20080319/dmri/dwi_orig.mghdti.bval > > > s > > > > > > > > > > > > > > > > > > > The format of the bvecs and bvals that you sent seems fine, but (and > > > this > > > > > has nothing to do with the error you're getting) I have to warn you that > > > > > you may not be able to get good results running probabilistic > > > tractography > > > > > on this data. It looks like you're acquiring the same 6 diffusion > > > > > directions, repeated 8 times. Six directions is the absolute minimum for > > > > > reconstructing the tensor model, but will probably not be sufficient for > > > > > the crossing fiber model that bedpostx reconstructs (and is used by > > > > > tracula). Your scan time is better spent acquiring 48 different > > > > > directions, rather than the same 6 directions 8 times. > > > > > > > > > > a.y > > > > > > > > > > On Mon, 29 Jul 2013, Borsodi Florian wrote: > > > > > > > > > > > Hello, > > > > > > > > > > > > I have been trying to run tracula on my data and i keep getting the > > > same > > > > > > kind of error repeatedly. > > > > > > For my imput I am using dicoms from a Siemens scanner with a stadard > > > > > > diffusion protocol. However, tracula cannot read the bvec and bval > > > data > > > > > out > > > > > > of the dicom header. Therefore, I implemented bvec and bval files into > > > > the > > > > > > config file. > > > > > > After doing so, I got the error which says that tracula cannot find > > > the > > > > > > "dwi_orig_flip.mghdti.bvecs" and "dwi_orig_flip.mghdti.bvals" files. > > > > > > I have tried many options, but still cannot find a solution. > > > > > > I am hoping to get some troubleshooting help. > > > > > > > > > > > > I have atteched my log- and config- files, as well as my bvec and bval > > > > > > files. > > > > > > To uphold patient confidentiality, I have encode the name patient's > > > data > > > > > as > > > > > > "AAAAAA". > > > > > > > > > > > > I believe the problems are the bvec and bval files or their > > > structures. > > > > > The > > > > > > log-file lete me assume this, especially the lines 202 - 205, 264 - > > > 268 > > > > > and > > > > > > 1480 - 1484. > > > > > > > > > > > > Thank you in advance for your help, and your speedy response. > > > > > > > > > > > > With kind regards, > > > > > > > > > > > > Florian Borsodi > > > > > > Department of Neurology > > > > > > Medical University of Graz > > > > > > > > > > > > > > > > > > > > > > > > > > > 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(a)nmr.mgh.harvard.edu > > > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > > > > > > > > > > > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >

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Raw Cortical thickness values
by Muhammad Naveed Iqbal Qureshi 06 Jul '17

06 Jul '17

Dear Community, I need to know how can I read the numeric cortical thickness values from freesurfer processed files. (as there are too many in the surf folder) Thank you. Best Regards Naveed

2 2

Average myelination within ROI
by SHAHIN NASR 06 Jul '17

06 Jul '17

Hi Surfers, I want to measure the average amount of myelinations within my ROI(s), I have already generated my myelination maps on surfaces (e.g. lh.myelin_ProjFrac0p5.nii ). Then I used mri_segstats as below: mri_segstats --i lh.myelin_ProjFrac0p5.nii --slabel SBJ_001 lh lh.V1 --sum V1_Stats.txt --accumulate but the numbers don't make any sense. For instance: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 0 125261 82573.4 Seg0000 110280.4453 0.2922 -5.5000 51.0000 56.5000 2 1 1138 764.8 Seg0001 941.0988 0.1572 0.2675 1.4203 1.1527 How can mean=941.0988 when the max=1.4203 ??? Regards -- Shahin Nasr PhD in Cognitive Neuroscience Martinos Imaging Center, MGH Harvard Medical School

2 1

mri_cvs_register failure from missing shared lib
by Michael Waskom 25 Apr '17

25 Apr '17

Hi, I had mri_cvs_register die on me when it couldn't find a shared library. Relevant bit is (full log is attached): mris_resample: error while loading shared libraries: libboost_program_options.so.5: cannot open shared object file: No such file or directory Freesurfer bugr info: -------------------- FREESURFER_HOME: /hsgs/software/freesurfer/5.3.0 Build stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 RedHat release: Red Hat Enterprise Linux Server release 6.3 (Santiago) Kernel info: Linux 2.6.32-358.6.2.el6.x86_64 x86_64 ---------------------- Any thoughts on how to proceed? Thanks! Michael

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Re: [Freesurfer] hello freesurfer developer~
by A-reum Min 27 Sep '16

27 Sep '16

hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu>: > don't use .hdr. When you have a .hdr/.img pair, just use the .img file. > > > On 9/16/15 10:51 AM, A-reum Min wrote: > > hello, experts > I have some question. > > I want to use analyze format instead of DICOM file. > > So, i type this sentence > > recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i > /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 > > > and then error occured.... > > ERROR: cannot determine file type for > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > How can i to do using analyze format? > > > 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve(a)nmr.mgh.harvard.edu>: > >> Specify something for --seg. It just needs to be a surface overlay of >> the same size as the input. >> >> On 08/27/2015 01:49 AM, A-reum Min wrote: >> > Hello doug >> > >> > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' >> > then, error occured --> ERROR: must specify a segmentation volume >> > >> > >> > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve(a)nmr.mgh.harvard.edu >> > <mailto:greve@nmr.mgh.harvard.edu>>: >> > >> > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 >> > >> > >> > On 8/26/15 9:22 PM, A-reum Min wrote: >> >> Hello developer, >> >> >> >> I have some question to you. >> >> >> >> How can i get the significant vertices value using Qdec result? >> >> >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> >> unknown. >> >> >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> >> >> How can i fix it? >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >> >>> Hello developers >> >>> >> >>> I have some question to you. >> >>> >> >>> 1.In fig.png, how many vertices were composed of cluster at >> >>> least? >> >> I'm not sure what you mean. it does not look like there are >> >> any clusters there >> >>> >> >>> 2. How to change Area Threshold(fig.png)? >> >> The area is controlled by the clusterwise threshold (--cwp) >> >> to mri_glmfit-sim >> >>> >> >>> 3. How to change CSD thresh(fig.png)? >> >> That is controlled by the threshold when specifying "--cache >> >> threshold sign" to mri_glmfit-sim >> >>> >> >>> 4. What is the difference between two words(Area Threshold, >> >>> CSD thresh)? >> >> One is the cluster-pvalue and the other is the >> >> cluster-forming thershold >> >>> >> >>> 5. What is the exactly mean two words(Area Threshold, CSD >> >>> thresh)? >> >> See above >> >> >> >>> >> >>> Thank you >> >>> >> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >> >>> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu >> >>: >> >>> >> >>> >> >>> >> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >> >>> > HI expert ! >> >>> > >> >>> > My name is Areum. I have some question to you. >> >>> > >> >>> > 1. Does FreeSurfer offer a effect size? if that offer, >> >>> how can i use >> >>> > effect size? >> >>> > >> >>> If you're doing a group analysis, you can compute >> >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >> >>> glmdir/contrast/effectsize.mgh >> >>> > >> >>> > 2. I was wondering about the stats.dat file in >> >>> stats_table (in Qdec >> >>> > folder). >> >>> > >> >>> > Stats.dat file’s value mean that each area’s average >> >>> (include whole >> >>> > vertex) or each >> >>> > >> >>> > area’s average (only significant vertex)? >> >>> > >> >>> what stats.dat? if subject/stats/lh.aparc.stats, then >> >>> the area is the >> >>> total area for the ROI >> >>> > >> >>> > 3. Can I get whole vertex value or significant vertex >> >>> value? Because, >> >>> > I want to >> >>> > >> >>> > compare two groups correlation using SPSS. In >> >>> addition, I want to compare >> >>> > >> >>> > thickness, volume and surface area correlation within >> >>> the one group >> >>> > using SPSS. >> >>> > >> >>> You can extract a given vertex with >> >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >> >>> vertexno.dat >> >>> vertexno.dat will be a text file with number of rows >> >>> equalt to thge >> >>> number of subjects where the value is the data from the >> >>> given (0-based) >> >>> vertex no. y.mgh is the input to mri_glmfit >> >>> > >> >>> > 4. I currently use the default cluster >> >>> size(significant area threshold >> >>> > is 0mm^2). So, I >> >>> > >> >>> > want to control cluster size larger than default >> >>> cluster size. How can >> >>> > I control the >> >>> > >> >>> > cluster size? >> >>> > >> >>> I don't know what you mean. >> >>> > >> >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >> >>> results. But when I >> >>> > use the >> >>> > >> >>> > both(GLM, Qdec) group analysis program results are not >> >>> same. What is >> >>> > differences >> >>> > >> >>> > between two analysis program? How can I get same >> >>> result while GLM and >> >>> > Qdec? >> >>> > >> >>> No way to know unless you tell us the specifics of what >> >>> you did >> >>> > >> >>> > 6. How can I get surface area and volume using >> >>> GLM(group analysis >> >>> > program)? >> >>> > >> >>> surface area and volume are outputs of recon-all, not glm >> >>> > >> >>> > >> >>> > plz reply to me >> >>> > >> >>> > >> >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >> >>> <naniyaah(a)gmail.com <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com >> >>>: >> >>> > >> >>> > Hello developer~ >> >>> > >> >>> > I have some questions to you. >> >>> > >> >>> > 1. Does FreeSurfer offer a effect size? if that >> >>> offer, how can i >> >>> > use effect size? >> >>> > >> >>> > 2. I was wondering about the stats.dat file in >> >>> stats_table (in >> >>> > Qdec folder). >> >>> > >> >>> > Stats.dat file’s value mean that each area’s >> >>> average (include >> >>> > whole vertex) or each >> >>> > >> >>> > area’s average (only significant vertex)? >> >>> > >> >>> > 3. Can I get whole vertex value or significant >> >>> vertex value? >> >>> > Because, I want to >> >>> > >> >>> > compare two groups correlation using SPSS. In >> >>> addition, I want to >> >>> > compare >> >>> > >> >>> > thickness, volume and surface area correlation >> >>> within the one >> >>> > group using SPSS. >> >>> > >> >>> > 4. I currently use the default cluster >> >>> size(significant area >> >>> > threshold is 0mm^2). So, I >> >>> > >> >>> > want to control cluster size larger than default >> >>> cluster size. How >> >>> > can I control the >> >>> > >> >>> > cluster size? >> >>> > >> >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >> >>> results. But >> >>> > when I use the >> >>> > >> >>> > both(GLM, Qdec) group analysis program results are >> >>> not same. What >> >>> > is differences >> >>> > >> >>> > between two analysis program? How can I get same >> >>> result while GLM >> >>> > and Qdec? >> >>> > >> >>> > 6. How can I get surface area and volume using >> >>> GLM(group analysis >> >>> > program)? >> >>> > >> >>> > >> >>> > thanks for your help >> >>> > >> >>> > >> >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >> >>> <naniyaah(a)gmail.com <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>>>: >> >>> > >> >>> > Hello bruce >> >>> > >> >>> > I solve this problem(12.png) >> >>> > >> >>> > Thank you >> >>> > >> >>> > 2015-07-27 13:03 GMT+09:00 dgw >> >>> <dgwakeman(a)gmail.com <mailto:dgwakeman@gmail.com> >> >>> > <mailto:dgwakeman@gmail.com >> >>> <mailto:dgwakeman@gmail.com>>>: >> >>> > >> >>> > Hi A-reum, >> >>> > >> >>> > I think you may be able to get a faster >> >>> response if you >> >>> > include some >> >>> > details about your setup: I would start >> >>> with the following: >> >>> > >> >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >>> > and run bugr. >> >>> > >> >>> > hth >> >>> > D >> >>> > >> >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >> >>> > > Hi, Bruce >> >>> > > >> >>> > > When i use a Qdec, this message(12.png) >> >>> show up.. >> >>> > > How can i solve this problem? >> >>> > > >> >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >> >>> > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >> >>> > > >> >>> > > 1. No, each subject has a different >> >>> #. You can map >> >>> > to fsaverage >> >>> > > (this is what -qcache does if you >> >>> specify it for >> >>> > recon-all), then >> >>> > > they will have the same #. >> >>> > > >> >>> > > 2. What result data do you mean? >> >>> > > >> >>> > > 3. Yes, although I'll leave the >> >>> details to Doug >> >>> > (since I don't >> >>> > > remember how his cluster code works). >> >>> > > >> >>> > > 4. The significance doesn't depend >> >>> on the cluster >> >>> > size unless you do >> >>> > > multiple comparison corrections (and >> >>> even then only >> >>> > if you do them a >> >>> > > certain way) >> >>> > > >> >>> > > cheers >> >>> > > Bruce >> >>> > > >> >>> > > >> >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >> >>> > > >> >>> > > HELLO developer >> >>> > > I have some question to you.. >> >>> > > >> >>> > > 1. Every patient is given to the >> >>> same number >> >>> > of vertex? >> >>> > > >> >>> > > 2. When i use a Qdec, How can I get >> the >> >>> > subject result data? >> >>> > > >> >>> > > 3. Could i get the significant >> vertex’s >> >>> > number, extent of the >> >>> > > significant area and gray matter volume? >> >>> > > >> >>> > > 4. Is it significant blue color >> >>> which how >> >>> > many connected >> >>> > > vertex? >> >>> > > >> >>> > > >> >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >> >>> > <naniyaah(a)gmail.com >> >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>> >> >>> > > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com <mailto: >> naniyaah(a)gmail.com>>>>: >> >>> > > hello developer~ >> >>> > > reconstruction is well done, so i'm >> >>> doing on >> >>> > 'qdec' step.. >> >>> > > Actually, i don't know how to treat the >> >>> Design >> >>> > menu exactly.. >> >>> > > >> >>> > >> >>> >> --------------------------------------------------------------------------- >> >>> > > Discrete(fixed factors) : diagnosis >> >>> > > continuous (covariate) : age , >> >>> > Left-Lateral-Ventricle >> >>> > > >> >>> > >> >>> >> --------------------------------------------------------------------------- >> >>> > > which one click before analyze? >> >>> > > >> >>> > > age range is 12years~24years/ >> >>> > > all subjects are adolescent. >> >>> > > and no outlier in age range.. >> >>> so.. age >> >>> > (continuous factor) does not >> >>> > > nasessart? >> >>> > > >> >>> > > >> >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >> >>> > <naniyaah(a)gmail.com >> >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>> >> >>> > > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com <mailto: >> naniyaah(a)gmail.com>>>>: >> >>> > > hello developer~ >> >>> > > reconstruction is well done, so i'm >> >>> doing on >> >>> > 'qdec' step.. >> >>> > > Actually, i don't know how to treat the >> >>> Design >> >>> > menu exactly.. >> >>> > > >> >>> > >> >>> >> --------------------------------------------------------------------------- >> >>> > > Discrete(fixed factors) : diagnosis >> >>> > > continuous (covariate) : age , >> >>> > Left-Lateral-Ventricle >> >>> > > >> >>> > >> >>> >> --------------------------------------------------------------------------- >> >>> > > which one click before analyze? >> >>> > > >> >>> > > >> >>> > > >> >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >> >>> > > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >> >>> > > I'm glad it worked out >> >>> > > Bruce >> >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >> >>> > > >> >>> > > Hello Bruce~ >> >>> > > You're right.. my PISA dicom file >> >>> > header >> >>> > > is too short >> >>> > > so, freesurfer didn't read it. >> >>> > > >> >>> > > Therefore I use another subjects >> >>> dicom >> >>> > > file and then freesurfer read it! >> >>> > > >> >>> > > thank you for u r adavice to me. >> >>> > > >> >>> > > I really appreciate u >> >>> > > >> >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >> >>> Fischl >> >>> > > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >> >>> > > Hi A-reum >> >>> > > >> >>> > > the problem is that newer >> >>> > versions >> >>> > > of scanner software compress >> >>> > > dicoms and the version of FS you >> >>> > > have doesn't know how to read >> >>> > > it. So you need to >> >>> decompress >> >>> > them >> >>> > > before passing them to >> >>> > > recon-all >> >>> > > >> >>> > > cheers >> >>> > > Bruce >> >>> > > On Sun, 5 Apr 2015, >> >>> A-reum Min >> >>> > > wrote: >> >>> > > >> >>> > > Hello developer~ >> >>> > > >> >>> > > Can you summarize what the >> >>> > > problem is? >> >>> > > ==> >> >>> > > my problem is recon-all -i >> >>> > > didn't working... >> >>> > > so, if i type the recon-all >> >>> > > -i~then show up theses >> >>> > > >> >>> > > >> >>> > > >> >>> > >> >>> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > ERROR: 32512, see >> >>> > > >> >>> > > >> >>> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out >> >>> > > for >> >>> > > more details >> >>> > > Linux localhost.localdomain >> >>> > > 2.6.32-504.el6.x86_64 #1 >> >>> > > SMP Wed Oct 15 04:27:16 >> >>> > > UTC 2014 x86_64 x86_64 >> >>> > > x86_64 GNU/Linux >> >>> > > >> >>> > > dcmdjpeg.fs: error while >> >>> > > loading shared libraries: >> >>> > > libijg8.so.3.6: cannot >> >>> > > open shared object file: No >> >>> > > such file or directory >> >>> > > >> >>> > > >> >>> > > >> >>> > >> >>> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > >> >>> > > then, i click the >> >>> > > >> >>> > > >> >>> root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, >> >>> > > show >> >>> > > up >> >>> > > these >> >>> > > dcmdjpeg.fs: error while >> >>> > > loading shared libraries: >> >>> > > libijg8.so.3.6: cannot >> >>> > > open shared object file: No >> >>> > > such file or directory >> >>> > > >> >>> > > Are you trying to read >> >>> > > compressed dicom? >> >>> > > ==> >> >>> > > Am i trying to read >> >>> > > compressed dicom? >> >>> > > I send my 10071579.dicom(i >> >>> > > use this) to you, >> >>> > > using -i, convert the dicom >> >>> > > file to mgh file. i just >> >>> > > know that dicom file >> >>> > > convert to mgz format using >> >>> > > -i /my data path >> >>> > > Is it right..?? >> >>> > > >> >>> > > >> >>> > > If so, Can you try running >> >>> > > dcmdjpeg on it to create >> >>> > > a new (uncompressed) >> >>> > > series and give that to >> >>> > > recon-all? >> >>> > > ==> (actually, i didn't >> >>> > > understand your sentence >> >>> > > means perfectly..) >> >>> > > zeke >> >>> > > >> >>> > >> >>> tomeaurl( >> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/c >> >>> > > >> >>> > > en >> >>> > > t >> >>> > > os6_x86_64/dcmdjpeg.fs) >> >>> > > and then, replace my >> >>> > > existing >> >>> > > >> >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs file. >> >>> > > Also, make sure it is set to >> >>> > > executable by typing >> >>> > > the following in a >> >>> > > terminal window: >> >>> > > $> chmod a+x >> >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs >> >>> > > >> >>> > > >> >>> > > 2015-04-05 2:30 GMT+09:00 >> >>> > > Bruce Fischl >> >>> > > >> >>> > > <fischl(a)nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>> >> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu> >> >>> > <mailto:fischl@nmr.mgh.harvard.edu >> >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >> >>> > > Hi A-reum >> >>> > > >> >>> > > sorry, I'm coming into >> >>> > > this late. Can you >> >>> > > summarize what the >> >>> > > problem is? Are you >> >>> > > trying to read compressed >> >>> > > dicom? If so, can >> >>> > > you try running >> >>> > > dcmdjpeg on it to create a new >> >>> > > (uncompressed) >> >>> > > series and give that >> >>> > > to recon-all? >> >>> > > >> >>> > > cheers >> >>> > > Bruec >> >>> > > >> >>> > > >> >>> > > >> >>> > > On Sat, 4 Apr 2015, >> >>> > > A-reum Min wrote: >> >>> > > >> >>> > > Hello >> >>> > > developers.. >> >>> > > >> >>> > > i type the >> >>> > > recon-all -i~then show up >> >>> > > theses >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > >> >>> >> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > ERROR: 32512, >> >>> > > see >> >>> > > >> >>> > > >> >>> > > >> >>> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out >> >>> > > for >> >>> > > more details >> >>> > > Linux >> >>> > > localhost.localdomain >> >>> > > 2.6.32-504.el6.x86_64 #1 >> >>> > > SMP Wed Oct 15 >> >>> > > 04:27:16 >> >>> > > UTC 2014 x86_64 >> >>> > > x86_64 x86_64 GNU/Linux >> >>> > > >> >>> > > dcmdjpeg.fs: >> >>> > > error while loading shared >> >>> > > libraries: >> >>> > > libijg8.so.3.6: >> >>> > > cannot >> >>> > > open shared >> >>> > > object file: No such file or >> >>> > > directory >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > >> >>> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > >> >>> > > error is occured >> >>> > > (a little differntly..) >> >>> > > then, i click >> >>> > > the >> >>> > > >> >>> > > >> >>> > > >> >>> root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, >> >>> > > show >> >>> > > up >> >>> > > these >> >>> > > >> >>> > > dcmdjpeg.fs: >> >>> > > error while loading shared >> >>> > > libraries: >> >>> > > libijg8.so.3.6: >> >>> > > cannot >> >>> > > open shared >> >>> > > object file: No such file or >> >>> > > directory >> >>> > > >> >>> > > i'm so sorry..to >> >>> > > bother you.. >> >>> > > >> >>> > > >> >>> > > >> >>> > > 2015-04-04 9:21 >> >>> > > GMT+09:00 A-reum Min >> >>> > > >> >>> > > <naniyaah(a)gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com> >> >>> > <mailto:naniyaah@gmail.com >> >>> <mailto:naniyaah@gmail.com>>>>: >> >>> > > hello >> >>> > > >> >>> > > i type the >> >>> > > recon-all -i~ >> >>> > > then show up >> >>> > > theses >> >>> > > >> >>> > >> >>> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > >> >>> > > >> >>> > > >> >>> > > +++++++ >> >>> > > >> >>> > > ERROR: 32256, >> >>> > > see >> >>> > > >> >>> > > >> >>> > > >> >>> /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out >> >>> > > for more details >> >>> > > Linux >> >>> > > localhost.localdomain >> >>> > > 2.6.32-504.el6.x86_64 #1 >> >>> > > SMP Wed Oct 15 >> >>> > > 04:27:16 UTC >> >>> > > 2014 x86_64 x86_64 x86_64 >> >>> > > GNU/Linux >> >>> > > >> >>> > >> >>> >> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > >> >>> > > >> >>> > > >> >>> > > +++++++ >> >>> > > the error is >> >>> > > occured (a little >> >>> > > differntly..) >> >>> > > then, i click >> >>> > > the >> >>> > > >> >>> > > >> >>> > > >> >>> /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, >> >>> > > show iuo these >> >>> > > >> >>> > > sh: >> >>> > > >> >>> > > /usr/local/freesurfer/bin/dcmdjpeg.fs: >> >>> > > >> >>> > > /lib/ld-linux.so.2: bad ELF >> >>> > > interpreter: No >> >>> > > such file or directory >> >>> > > >> >>> > > plz help me >> >>> > > 2015-04-04 4:12 >> >>> > > GMT+09:00 >> >>> > > >> >>> > > <zkaufman(a)nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@nmr.mgh.harvard.edu> >> >>> > <mailto:zkaufman@nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@nmr.mgh.harvard.edu>> >> >>> > > <mailto:zkaufman@nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@nmr.mgh.harvard.edu> >> >>> > <mailto:zkaufman@nmr.mgh.harvard.edu >> >>> <mailto:zkaufman@nmr.mgh.harvard.edu>>>>: >> >>> > > A-reum, >> >>> > > >> >>> > > Please >> >>> > > download the following >> >>> > > file: >> >>> > > >> >>> > > >> >>> > >> >>> >> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_ >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > x86_64/dcmdjpeg.fs >> >>> > > >> >>> > > And >> >>> > > replace your existing >> >>> > > >> >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs >> >>> > > file with >> >>> > > the >> >>> > > one from >> >>> > > the link above. Also, >> >>> > > make sure it is >> >>> > > set to >> >>> > > executable >> >>> > > by typing >> >>> > > the >> >>> > > following in a terminal >> >>> > > window: >> >>> > > >> >>> > > $> chmod >> >>> > > a+x >> >>> > > >> >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs >> >>> > > >> >>> > > And then >> >>> > > try again. >> >>> > > >> >>> > > -Zeke >> >>> > > >> >>> > > >> >>> > > > Hi >> >>> > > doug... recon-all dosen't >> >>> > > working.. >> >>> > > > >> >>> > > > If i >> >>> > > type the recon-all -i~ >> >>> > > > then, >> >>> > > error occured... >> >>> > > > >> >>> > > >> >>> > > >> >>> > >> >>> >> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > + >> >>> > > + >> >>> > > + >> >>> > > ++ >> >>> > > > >> >>> > > > JPEG >> >>> > > compressed, decompressing >> >>> > > > cd >> >>> > > >> >>> > > >> >>> > > >> >>> /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 >> >>> > > > >> >>> > > dcmdjpeg.fs +te >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm >> >>> > > > >> >>> > > >> >>> > > /tmp/root.tmp.decompressed.dcm.kBIYHL >& >> >>> > > > >> >>> > > >> >>> > > >> >>> > > >> >>> /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out >> >>> > > > ERROR: >> >>> > > 32512, see >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out >> >>> > > for >> >>> > > > more >> >>> > > details >> >>> > > > Linux >> >>> > > localhost.localdomain >> >>> > > >> >>> > > 2.6.32-504.el6.x86_64 #1 SMP >> >>> > > Wed Oct 15 >> >>> > > > 04:27:16 >> >>> > > UTC 2014 x86_64 x86_64 >> >>> > > x86_64 >> >>> > > GNU/Linux >> >>> > > > >> >>> > > > >> >>> > > recon-all -s subj01 exited with >> >>> > > ERRORS at >> >>> > > Fri Apr 3 >> >>> > > 10:39:27 >> >>> > > PDT 2015 >> >>> > > > >> >>> > > > For more >> >>> > > details, see the log >> >>> > > file >> >>> > > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > >> >>> >> /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log >> >>> > > > To >> >>> > > report a problem, see >> >>> > > > >> >>> > > >> >>> > > >> >>> > > >> >>> http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> >>> > > > >> >>> > > >> >>> > > >> >>> > >> >>> >> >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >> >>> > > + >> >>> > > + >> >>> > > + >> >>> > > +++ >> >>> > > > >> >>> > > > I copy >> >>> > > the libdcmjpeg.so.3.6 and >> >>> > > paste in >> >>> > > >> >>> > > FREESURFER_HOME/lib >> >>> > > > after >> >>> > > that type the setenv >> >>> > > LD_LIBRARY_PATH >> >>> > > >> >>> > > $FREESURFER_HOME/lib >> >>> > > > >> >>> > > > but.. >> >>> > > didn't working .. >> >>> > > > >> >>> > > > same >> >>> > > error occured --> >> >>> > > dcmdjpeg.fs: error >> >>> > > while loading >> >>> > > shared >> >>> > > libraries: >> >>> > > > >> >>> >> > ... > > [메일의 일부입니다.] > _______________________________________________ > 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 > 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. > >

3 27

-hippocampal-subfields-T1T2
by Daniele Orlandi 15 Jun '16

15 Jun '16

Dear All, I'm trying to run the flag -hippocampal-subfields-T1T2 with the new FS v6.0 but I get the following error: >Fitting mesh to synthetic image from ASEG took 217.8633 seconds >Transforming points >Transforming points >ltaReadFile(/media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta): can't open file >No such file or directory >ERROR: Reading transform from file /media/orlandi/Ub4_Shared_HD/orlandi/PharmaCog-Volontari/CARTELLE-avg+base+long+T2/out_v5.3_35-MRIT1-VO-003-T01-avg.long.base_v5.3_35-MRIT1-VO-003/mri/transforms/T1_to_T1+T2.v10.lta Do you have any suggestion? thank you all for your collaboration Daniele _______________________________________________________________________________ Daniele Orlandi, PsyD, Research Assistant Laboratory of Epidemiology, Neuroimaging Alzheimer IRCCS Centro San Giovanni di Dio, Fatebenefratelli Via Pilastroni 4 25125 Brescia - Italy tel:+39 030/3501563 cell: +39 3495119685 <%2B39%20030%2F3501563> email: dorlandi(a)fatebenefratelli.it; daniele.orlandi.psy(a)gmail.com (http://www.centroalzheimer.org/sito/chi_staff_e.php)

3 2

3T or nuintensitycor3t
by Kasper Jessen 12 Apr '16

12 Apr '16

Dear freesurfer, To clear up som confusion i would like to ask if there is a difference between adding a -3T or -nuintensitycor3t flag? Best regards, Kasper -- Kasper Jessen, MD, PhD student Center for neuropsychiatric Schizophrenia Research (CNSR) Mental Health Centre Glostrup Nordre Ringvej 29-67 2600 Glostrup Tlf.: 24430136 E-mail: kasper_j(a)cnsr.dk eller kasper.jessen(a)regionh.dk

2 3

FSFAST mkcontrast-sess with spmhrf 2 question
by Joseph Dien 25 Mar '16

25 Mar '16

Hi, I have a question about how mkcontrast-sess works. I ran an analysis using the mkanalysis-sess option spmhrf 2 so there are three regressors for each predictor, the primary, the latency, and the dispersion. When specifying the contrast weights for mkcontrast-sess, the documentation indicates that they are specified in terms of the conditions as numbered in the paradigm file, not the individual regressors. Furthermore there only appears to be one contrast value output for each contrast, not three. How are the three regressors being handled? I can think of several scenarios: 1) the contrast weights are not actually in terms of conditions (the documentation is incorrect), they are actually in terms of the regressors (so contrasting conditions 1 and 2 could be specified as -a 1 -a 2 -a 3 -c 4 -c 5 -c 6). 2) the latency and dispersion regressors are being ignored (a common practice). The contrast weights should therefore be specified as -a 1 -c 2. 3) The Calhoun et al (2004) approach is being used to combine the three regressors into a "derivative boost" amplitude measure. The contrast weights should therefore be specified as -a 1 -c 2. Thanks for any help you can give me! Joe -------------------------------------------------------------------------------- Joseph Dien, Senior Research Scientist University of Maryland E-mail: jdien07(a)mac.com Phone: 202-297-8117 http://joedien.com//

2 17

Re: [Freesurfer] epidewarp.fsl for FSL 5.x
by Douglas Greve 22 Mar '16

22 Mar '16

It is there again. I don't know what the status if it is in terms of the version. Try it and let me know doug On 11/25/14 4:34 PM, Morgan Hough wrote: > Hi Doug, > > Could you put the epidewarp.fsl script back on your ftp site? I don’t > see it at the link in the archives: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/epidewarp.fsl > > BTW, is the script updated in some way for 5.x or can I can the old > script just be changed to accept 5.x version numbers. > > Cheers, > > -Morgan

5 10

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Freesurfer November 2015