Freesurfer

freesurfer@nmr.mgh.harvard.edu

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30078 discussions

Do you suggest to denoise T1 before feed it to Freesurfer
by Zhengchen Cai 27 Sep '16

27 Sep '16

Hi Freesurfers, In order to get the better segmentation and surfaces by Freesurfer, do you think it is necessary to denoise T1 before feed it to Freesurfer? Since there are several advanced MRI denoising methods which are not covered in FS preprocessing, I though it would be better to perform one of them before FS. However, one of my concern is that those denoising will modify the intensity of the image and this may effect or even conflict with the processing in FS such as intensity normalization or registration to the template. Based on my experiences of FSL, most of time, the denoising methods will make the segmentation worse. For FS, I've tried just few subjects and the segmentations were better than feeding the raw MRIs. What is your suggestion in general case? or maybe it is not reasonable at all to denoise before FS? Many thanks. Best regars, Zhengchen

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Freeview Loading Volumes
by Robert Kraft 27 Sep '16

27 Sep '16

I use Freeview on a daily basis as my primary image viewer. I like it a lot and found it to be tremendously useful. I am usually interested in opening images in the current directory where I launched Freeview from the command line. I know you can load multiple images at once from the command line but occasionally I want to load an additional image. Ideally, I would like Freeview when I want to load a volume to open up the file explorer tool in the current directory. Instead, it opens up in another directory and I have to click down several directories before finding the file that I want. Freeview has been consistently opening up in the same directory. I just can’t figure out why it picks that directory. If someone could tell me if it is possible for Freeview to open the file browser in the directory it was launched I would be extremely grateful. Thanks for your help in advance, Bob

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Coordinates of particular volumes
by Aziz Nanthaamornphong 27 Sep '16

27 Sep '16

Dear Freesurfer experts, How can we get the coordinates (X, Y, Z) of a particular volume? I couldn't find any functions or command to do that. Thank you in advance. Aziz.

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Re: [Freesurfer] Coordinates of particular volumes (fwd)
by Douglas Greve 27 Sep '16

27 Sep '16

the command should be [i,j,k] = ind2sub(mri.volsize,pos); ---------- Forwarded message ---------- Date: Tue, 27 Sep 2016 13:00:51 +0700 From: Aziz Nanthaamornphong <aziz.n(a)phuket.psu.ac.th> Reply-To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> To: Freesurfer support list <freesurfer(a)nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Coordinates of particular volumes I have tried to get the coordinates with following commands: mri = MRIread('aseg.mgz'); pos = find(mri.vol == 17); [i,j,k] = ind2sub(10213,pos); However, I found that all values of 'j' are 1. is there something wrongs with my strategy? Best Regards, Aziz. On Mon, Sep 12, 2016 at 8:40 PM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Aziz, make sure $FREESURFER_HOME/matlab is in your matlab path. cheers Bruce On Mon, 12 Sep 2016, Aziz Nanthaamornphong wrote: Which the version of Matlab has a 'MRIread' function? I got this error message from my installed Matlab (v. 8.4.0). "Undefined function 'MRIread' for input arguments of type 'char'." Best Regards, Aziz. On Mon, Sep 5, 2016 at 6:46 AM, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: yup, or mri_Info called form the command line. If you use MRIread on the aseg.mgz you can extract e.g. the left hippocampus using matlab via: mri = MRIread('aseg.mgz'); find(mri.vol == 17); then compute the ras coords of those indices using ind2sub cheers Bruce On Sun, 4 Sep 2016, Ruyuan Zhang wrote: Hi, Aziz You can use MRIread function to read in a volume (i.e. brainmask.mgz). You will get a structure, which contains a field called ras2vox. cheers ruyuan On 9/4/16 6:23 PM, Aziz Nanthaamornphong wrote: Hi, For example, I want to know the list of x, y, z coordinates of a left hippocampus volume. As you mentioned "ras2vox" matrices, hoe can I see or get these matrices? Thank you. Aziz On Monday, 5 September 2016, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: Hi Aziz can you elaborate? What coordinates do you want? What are you trying to do with them? The .mgz format contains ras2vox matrices that let you go from voxel indices to RAS coordinates and such. cheers Bruce On Sun, 4 Sep 2016, Aziz Nanthaamornphong wrote: Dear Freesurfer experts, How can we get the coordinates (X, Y, Z) of a particular volume? I couldn't find any functions or command to do that. Thank you in advance. Aziz. -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz _______________________________________________ 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-mai l contains patient information, please contact the Partners Compliance HelpLin e at http://www.partners.org/complianceline . If the e-mail was sent to you in er ror but does not contain patient information, please contact the sender and prop erly 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 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. -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz _______________________________________________ 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. -- Aziz Nanthaamornphong, Ph.D., Chair of Master of Science Program in Information Technology Department of ICT Faculty of Technology and Environment Prince of Songkla University, Phuket Campus +66 7627 6716 (v) http://research.te.psu.ac.th/aziz

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QDEC error writing fsgd and generating contrasts
by Mürner-Lavanchy, Ines 27 Sep '16

27 Sep '16

Dear FreeSurfer Developers, I have the following problem and would be very happy if you could help me. I have searched the list and did not find the solution to my problem. I am using FS 5.1 because I have to reanalyze data which I preprocessed in 2014. Back then recon-all and all the group analyses worked fine. I only have the problem now since we have reinstalled FS. I computed a group analysis using QDEC (the same analysis as I did in 2014), but i get the following errors (/.../ is a place holder for my directory). qdec.table.dat and levels worked all fine before. ERROR: QdecGlmDesign::WriteFsgdFile: could not open /.../qdec.fsgd for writing when I press analyze again, this error occurs: ERROR: QdecProject::CreateGlmDesign: could not generate contrasts when I analyze again, the analysis starts to run until the following comes up MatrixWriteTxt(/.../lh-Avg-Intercept-thickness/C.dat) - file open failed Permission denied mghWrite(/.../lh-Avg-Intercept-thickness/gamma.mgh, -1): could not open file mghWrite(/.../lh-Avg-Intercept-thickness/gammavar.mgh, -1): could not open file mghWrite(/.../lh-Avg-Intercept-thickness/F.mgh, -1): could not open file mghWrite(/.../lh-Avg-Intercept-thickness/cnr.mgh, -1): could not open file mghWrite(/.../lh-Avg-Intercept-thickness/sig.mgh, -1): could not open file maxvox sig=1e+10 F=7409.8 at index 28 0 0 seed=1475358237 Segmentation fault But in the end, when I press analyze again, qdec runs the glm and the results are the same as when I did the same group analysis back in 2014 (without any error messages then). Do you have an idea what could be my problem? Thank you very much in advance, InLava uname -a: Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux

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QDEC error writing fsgd and generating contrasts
by Mürner-Lavanchy, Ines 27 Sep '16

27 Sep '16

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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

Re Re: Question regarding mri_convert
by Tamara Tavares 26 Sep '16

26 Sep '16

Thank you Bruce! Theoretically, I should get the same results if I pass my nii file through the recon-all command if I converted my dicom/IMA file into a nii using Slicer4 or the mri convert command? I did this and I got different volumes. Thank you, Tamara

2 1

Regional White Matter Hypointensity Volumes
by Bharadwaj, Pradyumna - (prad) 26 Sep '16

26 Sep '16

Hello Freesurfers, I am interested in obtaining the regional volumes of white matter hypointensities. What volume would I use a reference for obtaining the 'regions' ? and what commands would I need to use to obtain these regional volumes ? ?If there isn't an appropriate white matter volume that can be used as a reference, then is there a way to divide a subject's brain image or white matter volume image into say 8 equal quadrants, which can then be used as masks to obtain regional WMH volume in these quadrants? Thanks, -Prad

1 0

Re: [Freesurfer] Software License for Industry
by zkaufman＠nmr.mgh.harvard.edu 26 Sep '16

26 Sep '16

The FreeSurfer Software License Agreement does not contain any language explicitly or implicitly preventing commercial usage, however I will highlight the following text from the License Agreement: "Any commercialization of the Software is at the sole risk of the party or parties engaged in such commercialization In short, commercial entities seeking to make use of FreeSurfer should seek their own legal council on the interpretation of the license for their specific circumstance. -Zeke > Dear FS experts > > I have one concern regarding the license and the Freesurfer usage on > industry. > > We are setting up a start-up specialized with the analysis of brain MRI > and > we are interested on using FreeSurfer package as our main neuroimaging > tool, due to the large amount of utilities it provides. > > After reading carefully the Software License provided here ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferSoftwareLicense) it is > not clear for me if we could use yours software to provide a service to an > external organisation/customer for which payment will be received. > > Could someone provide some insight on this issue? > > Bests, > Joss. >

1 0

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