Freesurfer August 2016

freesurfer@nmr.mgh.harvard.edu

127 participants
198 discussions

Help on "mris_anatomical_stats"
by Lim, Lena 06 Apr '17

06 Apr '17

Dear Experts, I ran a group analysis in Qdec for the left volume and found a region of significant group difference. I wanted to extract this ROI. I defined this label and used the "map label to subjects" option in Qdec and ran the following but encountered the following error. Please kindly help... [spjwker@nanlnx2 FSL]1% mris_anatomical_stats -l lh.HCA_vol.label \-b -f PAC07/stats/lh.HCA_vol.stats PAC07 lh limiting computations to label lh.HCA_vol.label. reading volume /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/mri/wm.mgz... reading input surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... reading input pial surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.pial... reading input white surface /home/spjwker_PAC/Lena/CT_SA/FSL/PAC07/surf/lh.white... Segmentation fault Many thanks, Lena

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ExploreDTI Workshop!
by Szabolcs David 02 Apr '17

02 Apr '17

Thrilled to announce that we are going to hold an ExploreDTI workshop in Utrecht (July 4-6)! More details can be found here: http://www.exploredti.com/workshop. We hope to see you there! Cheers, Szabolcs

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Inflation of one hemi only
by Kang, XJ 10 Mar '17

10 Mar '17

Hi, I am trying to inflate right hemisphere only using the commands: recon-all -autorecon2 -hemi rh -subjid 160526 recon-all -autorecon3 -hemi rh -subjid 160526 The inflation stopped at the step: mris_volmask --label_left_white 2 --label_left_ribbon 3 --label_right_white 41 --label_right_ribbon 42 --save_ribbon 160526 SUBJECTS_DIR is /home/sata3/FreeSurfer/Subjects MRISread(/home/sata3/FreeSurfer/Subjects/160526/surf/lh.white): could not open file The program "mris_volmask" needs to read "lh.white", which is not generated. Any expert has any suggestions? Maybe I didn't use the commands correctly? Thank you for your help. XJ Kang

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Cerebral (without ventricles) Volume = aseg.stats / SupraTentorialNotVent ?
by Kaiming Yin 21 Feb '17

21 Feb '17

Dear guys, Could I ask which value in the stats/aseg.stats represents the volume of the cerebrum (including the subcortical structures while excluding the ventricles and brain stem)? I'm not sure whether the "SupraTentorialNotVent" can be the value for this measurement, and could it be a bit bigger than the real value due to the partial volume effect? Besides, could I also ask is there a value represent the volume of the cerebellum? Currently I calculate the volume by adding the left/right cerebellar GM/WM values in the detailed list in aseg.stats file. Many thanks, Kaiming

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'Invalid' license file
by Lee.Reid＠csiro.au 16 Nov '16

16 Nov '16

Hi, Our IT department have recently upgraded our cluster OS and now Freesurfer complains that its license is invalid. I have tried rebuilding, and acquiring a new license, but these do not fix the problem. The license file I am using works in my Ubuntu 12.04 computer - it has been copied across as a file, not via a text editor - and used to work on an older version of the same OS. Do you know of any solution to this issue? I've tried everything I have seen on the mailing list, including naming it .license and license.txt, checking for whitespace, etc. Our OS is now SUSE Linux Enterprise Server 12 SP1 (x86_64). Many thanks, Lee

3 4

Mean intensity with mri_segstats : different results with .annot or .label
by Matthieu Vanhoutte 11 Nov '16

11 Nov '16

Dear experts, I am in trouble with two ways of computing mean intensity with mri_segstats. First I have used on .annot files with three different labels inside (SegId 1 to 3) : *mri_segstats --annot fsaverage lh cache.th23.pos.sig.ocn.annot --i lh.PET.fsaverage.sm10.mgh --sum lh.pet.sum* which give me those results: # ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range 1 1 27805 14182.6 cluster-001 8.8194 1.4351 6.2105 14.2947 8.0842 2 2 2321 1047.3 cluster-002 10.3661 1.0848 8.8375 12.9317 4.0942 3 3 552 313.1 cluster3 10.3365 0.4711 9.3719 11.8694 2.4975 Second I have created on .label files containing the three segmented labels (SegId 1 to 3) and used this label with mri_segstats: *mri_segstats --slabel fsaverage lh lh.th23.cluster.thresh1.3.label --i lh.PET.fsaverage.sm10.mgh --excludeid 0 --sum lh.pet.label.sum * which give me those results: *# ColHeaders Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range * * 1 1 30678 15542.9 Seg0001 8.9637 1.4701 6.2105 14.2947 8.0842 * I verified if I obtained the same results with the two ways (.annot or .label) and everything is fine comparing NVertices, Area_mm2 but Mean in first way gives me (8.8194+10.3661+10.3365)/3 = 9.84066 and with .label file Mean = 8.9637. Did I have miss anything and how is computed mean intensity ? Many thanks in advance. Best regards, Matthieu

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Multiple Comparison Question for surface-based analyses
by Ajay Kurani 28 Oct '16

28 Oct '16

Hello Freesurfer Experts, Recently there were two article published regarding clusterwise simulations for volumetric fmri analyses and potential errors for underestimating clusterwise extent thresholds. 1) http://www.pnas.org/content/113/28/7900.full.pdf?with-ds=yes 2) biorxiv.org/content/early/2016/07/26/065862 One issue pointed out from these articles seems software specific, however the second issue is determining the proper clustersize. The heavy-tail nature of spatial smoothness seems to be ignored and a gaussian shape is generally assumed, leading to an underestimation of the spatial smoothness which can affect cluster size calculations. The issues are highlighted in the second article above. I created my own monte carlo simulation in Freesurfer for a specific brain template and I wanted to find out if these concerns also apply to my surface based simulations? I am not sure if it does since the monte carlo tool is a GRF simulation as opposed to an analytic equation, however given that these articles were highlighted very recently, I wanted to ensure I am running things appropriately for surface based cortical thickness/dti analyses. Thanks, Ajay

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Interpretation of QA tools results
by Matthieu Vanhoutte 21 Oct '16

21 Oct '16

Dear FS experts, Could you explained me how to interpret results from the QA tools. Please find attached the recon_checker summary log. 1) How to know there is a problem according to results below: *checking subcortical label: Left-Cerebral-Exterior, 0 +/-* *checking subcortical label: Left-Cerebral-White-Matter, 0 +/-* *checking subcortical label: Left-Cerebral-Cortex, 0 +/-* *checking subcortical label: Left-Lateral-Ventricle, 1.77932 +/-* *checking subcortical label: Left-Inf-Lat-Vent, 0.115084 +/-* *checking subcortical label: Left-Cerebellum-Exterior, 0 +/-* *checking subcortical label: Left-Cerebellum-White-Matter, 0.768042 +/-* *checking subcortical label: Left-Cerebellum-Cortex, 2.50118 +/-* *checking subcortical label: Left-Thalamus, 0 +/-* *checking subcortical label: Left-Thalamus-Proper, 0.324235 +/-* *checking subcortical label: Left-Caudate, 0.190688 +/-* *checking subcortical label: Left-Putamen, 0.24631 +/-* *checking subcortical label: Left-Pallidum, 0.0782828 +/-* *checking subcortical label: 3rd-Ventricle, 0.127606 +/-* *checking subcortical label: 4th-Ventricle, 0.0697322 +/-* *checking subcortical label: Brain-Stem, 1.2108 +/-* *checking subcortical label: Left-Hippocampus, 0.191568 +/-* *checking subcortical label: Left-Amygdala, 0.0665945 +/-* *checking subcortical label: Left-Insula, 0 +/-* *checking subcortical label: Left-Operculum, 0 +/-* *checking subcortical label: Line-1, 0 +/-* *checking subcortical label: Line-2, 0 +/-* *checking subcortical label: Line-3, 0 +/-* *checking subcortical label: CSF, 0.0903738 +/-* *checking subcortical label: Left-Lesion, 0 +/-* *checking subcortical label: Left-Accumbens-area, 0.0259807 +/-* *checking subcortical label: Left-Substancia-Nigra, 0 +/-* *checking subcortical label: Left-VentralDC, 0.196737 +/-* *checking subcortical label: Left-undetermined, 0 +/-* *checking subcortical label: Left-vessel, 0.0043689 +/-* *checking subcortical label: Left-choroid-plexus, 0.0806885 +/-* 2) When looking at the white matter QA, three colors are used: red (pial surface ?), yellow (white surface ?) and green (?). Does it make sense to verify all colored surfaces or only the white matter surface in this WM QA ? How to decide when rejecting bad preprocessed subject ? Best regards, Matthieu

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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

Z-stat - z.mgh
by Robby De Pauw 16 Sep '16

16 Sep '16

Dear FreeSurfer users I am not able to extract the Z-values as they are not present in my output: z.mgh -- z-stat that corresponds to the significance Are these Z-values always produced (or only in case of two group comparison)? Is there a way to produce this map myself? This is my output after fitting the model (mri_glmfit) and after clusterwise correction for MC: C.dat cache.th13.abs.sig.voxel.mgh F.asc cache.th13.abs.y.ocn.dat F.csv cnr.mgh F.mgh gamma.mgh cache.th13.abs.pdf.dat gammavar.mgh cache.th13.abs.sig.cluster.mgh maxvox.dat cache.th13.abs.sig.cluster.summary sig.asc cache.th13.abs.sig.masked.mgh sig.csv cache.th13.abs.sig.ocn.annot sig.mgh cache.th13.abs.sig.ocn.mgh I am currently working on the latest version of FreeSurfer: freesurfer-Darwin-lion-stable-pub-v5.3.0 Thank you for your response, Greetings Robby Robby De Pauw, PT, MT, drs. T +32 09 332 12 19 | Email Robby.DePauw(a)Ugent.be<mailto:Robby.DePauw@ugent.be> Ghent University | Rehabilitation Sciences and Physiotherapy Campus Heymans 3B3 (022) De Pintelaan 185 BE-9000 Ghent Route to my office<https://soleway.ugent.be/routes/1090>

2 2

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Freesurfer August 2016