Freesurfer

freesurfer@nmr.mgh.harvard.edu

1 participants
30089 discussions

Sourcing error?
by jwaugh＠nmr.mgh.harvard.edu 18 Jul '12

18 Jul '12

Hello, I am having difficulty with an fMRI command line program that we have run successfully in the past, but which we haven't used in ~4 months. In response to the following command lines (from a csh script): "setenv FSL_DIR $FSLDIR source /usr/local/freesurfer/nmr-stable3-env source ${FSLDIR}/etc/fslconf/fsl.csh setenv FSLOUTPUTTYPE ANALYZE setenv SUBJECTS_DIR /cluster/ablood/1/R01_Botox cd /cluster/ablood/1/R01_Botox preproc-sess -s CD_R01BTX_CTRL7_sess1 -df sessdirfile -mcout fmc5 -fwhm 5 -smin fmc5 -smout fmcsm5 preproc-sess -s CD_R01BTX_CTRL7_sess1 -df sessdirfile -mcout fmc4 -fwhm 4 -smin fmc4 -smout fmcsm4 mkanalysis-sess.new -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -TR 2.5000 -paradigm 60_60_60_60_60_60_60.para -designtype blocked -funcstem fmcsm5 -motioncor -runlistfile runlistfile_tap_lh_long -inorm -tpef tpexclude60_60_60_60_60_60_60 -nconditions 1 -timewindow 25.0000 -gammafit 2.25 1.25 -s CD_R01BTX_CTRL7_sess1 -df sessdirfile selxavg-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -s CD_R01BTX_CTRL7_sess1 -df sessdirfile mkcontrast-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -contrast tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5_contrast -a 1 -c 0 stxgrinder-sess -analysis tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5 -contrast tap_lh_long_CD_R01BTX_CTRL7_sess1_sm5_contrast -s CD_R01BTX_CTRL7_sess1 -df sessdirfile" we get the following error messages: ERROR: cannot find /usr/pubsw/packages/fsl/current/bin/ip ERROR: ipfsl failed ERROR: spatialsmooth-sess failed In the past such an error has resulted from using the newer source environment (stable-5.1), but would always work when sourced with stable-3. I have re-run this with stable-5.1 as well, but we get the same type of error. Any help would be much appreciated! Thanks, Jeff

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Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
by Douglas N Greve 18 Jul '12

18 Jul '12

It should be the sig.mgh file in your contrast directory. doug ps. Please post to the list and not me directly. thanks! On 07/18/2012 11:56 AM, Antonella Kis wrote: > Hi Doug, > > Many thanks for your prompt response and your help. I have one more > question please. I searched for mri_surfcluster command and I am not > sure what should be my input file. > > Can you please clarify this for me? Should this be L-frontal.fsgd > since I have more subjects? > > > Thank you. > Antonella > > ------------------------------------------------------------------------ > *From:* Douglas N Greve <greve(a)nmr.mgh.harvard.edu> > *To:* freesurfer(a)nmr.mgh.harvard.edu > *Sent:* Wednesday, July 18, 2012 11:39 AM > *Subject:* Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option > > Hi Antonella, first of all, FDR and clusterwise correction are doing > different things. Technically, you don't get clusters from FDR. FDR will > choose a voxel-wise threshold for you, and any voxel above threshold can > be interpreted as surviving FDR (but you should know how to interpret it > -- see Tom Nichols' paper). Of course, many of the voxels may appear as > clusters. In your case, FDR found a voxel-wise threshold of 3.8 > (meaning p<1.5849e-04). The fastest way to get the values you want is > to go outside of QDEC. First, run mri_surfcluster using a threshold of > 3.8 (--thmin 3.8). Specify an output cluster number map (--ocn ocn.mgh) > and a summary file (--sum sum.dat). This will produce a lot of > "clusters", two of which should be the ones below (you can prune the > list by specifying that the clusters need to be a certain size > (--minarea). Once you have the ocn file, you can run mri_segstats, > something like > mri_segstats --seg ocn.mgh --i y.mgh --avgwf avgwf.dat --excludeid 0 > y.mgh is the glmfit input file created by qdec. This will produce > avgwf.dat which will have a column for each cluster, the order will be > the same as that in sum.dat. > > douig > > On 07/18/2012 11:25 AM, Antonella Kis wrote: > > Dear FS team, > > > > > > > > I am doing a cortical thickness study using QDEC. I used FDR and got > > the following clusters: > > > > Generating cluster stats using min threshold of 3.8... > > Found 2 clusters > > Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 > > ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation > > --------- --- ------ --------- ---- ---- ---- ----- ---------- > > 1 -3.8743 18231 4.55 -39.8 1.5 14.1 14 precentral > > 2 -3.8065 47386 2.66 -8.2 33.1 33.9 4 > superiorfrontal > > ============================================================ > > I need to get the cortical thickness values from each subject within > > this clusters so I am trying to use > > mri_glmfit-sim with --cache option and I wonder what value should I > > choose in this case for cache (2, 3.3 or 4) > > and what --cwpvalthresh 0.05 or .025 to get the same results as FDR's > > results. > > > > I tried: > > mri_glmfit-sim \ > > --glmdir lh.L_frontal.glmdir \ > > --cache 3 neg \ > > --cwpvalthresh .05 \ > > --overwrite > > > > # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP > > CWPLow CWPHi NVtxs Annot > > 1 -3.874 18231 320.36 -39.8 1.5 14.1 0.02610 > > 0.02410 0.02820 949 precentral > > 2 -3.807 47386 700.61 -8.2 33.1 33.9 0.00020 > > 0.00000 0.00040 1053 superiorfrontal > > > > so as you can see the clusters are the same but their Size and NVtxs > > is so different. What is wrong? > > > > Thank you for your time and help. > > Antonella > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@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. > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] ask for help
by Douglas N Greve 18 Jul '12

18 Jul '12

Hi Haochuanxi, what is the context of this question? Are you running a qdec analysis? What are your variables? doug ps. Please post your questions to the freesurfer list instead of me directly. thanks! On 07/18/2012 11:55 AM, 传玺 wrote: > Dear Doulgus > Could you tell me the exactly meaning of "a significant group by > gender interaction was found ", that is, what is the meaning of "group > by gender interaction "? > I know it is not your duty to answer this question, but it is > important to understand that concept to me, so I would be grateful to > you if you lend me a hand! > BEST WISHES! > Haochuanxi > Peking University China > > > 来自网易手机邮箱了解更多 <http://shouji.163.com> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve(a)nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Re: [Freesurfer] FDR versus mri_glmfit-sim with --cache option
by Antonella Kis 18 Jul '12

18 Jul '12

Hi Doug, Many thanks for your prompt response and your help. I have one more question please. I searched for mri_surfcluster command and I am not sure what should be my input file. Can you please clarify this for me? Should this be L-frontal.fsgd since I have more subjects? Thank you. Antonella

1 0

FDR versus mri_glmfit-sim with --cache option
by Antonella Kis 18 Jul '12

18 Jul '12

Dear FS team, I am doing a cortical thickness study using QDEC. I used FDR and got the following clusters: Generating cluster stats using min threshold of 3.8... Found 2 clusters Contrast: 'lh-Diff-Class1-Class2-Intercept-thickness', 15fwhm, DOF: 69 ClusterNo Max VtxMax Size(mm2) TalX TalY TalZ NVtxs Annotation --------- --- ------ --------- ---- ---- ---- ----- ---------- 1 -3.8743 18231 4.55 -39.8 1.5 14.1 14 precentral 2 -3.8065 47386 2.66 -8.2 33.1 33.9 4 superiorfrontal ============================================================ I need to get the cortical thickness values from each subject within this clusters so I am trying to use mri_glmfit-sim with --cache option and I wonder what value should I choose in this case for cache (2, 3.3 or 4) and what --cwpvalthresh 0.05 or .025 to get the same results as FDR's results. I tried: mri_glmfit-sim \ --glmdir lh.L_frontal.glmdir \ --cache 3 neg \ --cwpvalthresh .05 \ --overwrite # ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.874 18231 320.36 -39.8 1.5 14.1 0.02610 0.02410 0.02820 949 precentral 2 -3.807 47386 700.61 -8.2 33.1 33.9 0.00020 0.00000 0.00040 1053 superiorfrontal so as you can see the clusters are the same but their Size and NVtxs is so different. What is wrong? Thank you for your time and help. Antonella

2 1

sum of WM and GM coming out to be bigger than ICV after recon-all
by Ayaz, Muhammad 18 Jul '12

18 Jul '12

Dear All, After running recon-all, I noticed several subjects that sum of WM and GM is bigger than ICV. I have re-run these subjects and the results is the same sum of GM and WM is coming out to be bigger than ICV. Any suggestions? I need to calculate normalized volumes. Regards Ayaz The information contained in this message and any attachments is intended only for the use of the individual or entity to which it is addressed, and may contain information that is PRIVILEGED, CONFIDENTIAL, and exempt from disclosure under applicable law. If you are not the intended recipient, you are prohibited from copying, distributing, or using the information. Please contact the sender immediately by return e-mail and delete the original message from your system.

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Labels for comparison
by John Drozd 18 Jul '12

18 Jul '12

Hello, I have successfully developed an automated algorithm combining pixel intensity-based and shape based approaches to segment the lateral ventricles. I have applied my algorithm to a small data set of 1.5 T1 ADNI images consisting of 24 AD (subjects with Alzheimer Disease) 19 MCI (subjects with Mild Cognitive Impairment) and 24 NEC (elderly controls). In my cases, particularly AD cases, I noticed that the segmentation of the lateral ventricles is connected to the third ventricle with foramina (usually 1 on a side or on both sides). Also, sometimes I find a connection with the posterior horn and third ventricle. I have researched CSF flow and from the literature, and all of these are real connections. I am near completion of developing an automated cropping scheme with a colleague to crop the third ventricle at these junctions. Our implementation is a combination of C++ code that we have developed and modified ITK classes. We have been viewing our segmented label maps in Slicer3 and generated 3D renderings using Slicer3's Model Maker module which is based on Marching Cubes. I have viewed a Freesurfer segmentation in Slicer3 based on a tutorial on the Slicer web site. I presented a poster of our results at the AIC and AAIC conference which I am at now in Vancouver, and a few people have asked me to compare my volumes with other methods. They were particularly interested in comparing my volumes with Freesurfer ventricle volumes and cross-sectional and longitudinal data. I was told and found csv files on the ADNI web site of Freesurfer analysis. I plan to correlate my values with Freesurfer's values, but I would be interested if Freesurfer also finds these connections between the third ventricle and lateral ventricles and also if it includes isolated temporal horn pieces when the horns are discontinuous due to the MRI not being able to resolve a very thin portion of the temporal horn. So, would it be possible, if I gave you a list of my ADNI subjects, for you to provide me the freesurfer label maps that correspond to the volumes in the csv files that are on the ADNI web site please? I could run Freesurfer but I would prefer having the label maps that exactly correspond to the Freesurfer ventricle volumes that are on the ADNI website. These would be from the two versions of Freesurfer noted on the ADNI web site in the ADNI Study Data/MRI image analysis link. Thank you, John Sent from my iPhone 4S

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Flip brain
by Tadeu Kubo 18 Jul '12

18 Jul '12

Hi Dear FS experts, Doug sent these links, but I can't download them. Do you have the new links? Download these filesftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/surfregf… Thank you. Regards, Tadeu

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Hc segmentation: crosssectional stream with v4.5, longitudinal with v5.1
by Wenger, Elisabeth 17 Jul '12

17 Jul '12

Dear FreeSurfer experts, we have processed a dataset crossectionally within version 4.5, and then ran the longitudinal stream with v5.1. we are interested in the hippocampus segmentations and now i'm wondering whether i should go back and run the whole analysis from scratch with the newest version. I understand that it might or even will give me slightly different results, but would it also be the assumption that the new results would be somewhat more correct, that is anatomically more accurate, because maybe for example the processing has been optimized for hippocampal segmentation or anything like that in the newer version? Or would they just be different, as they would also be different when running it on a different computer, Mac or PC, OSX version, etc? Thank you very much for your help in advance!! Best wishes, Elisabeth

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I had a Computer Failure, how can I resume recon-all for base (longitudinal processing)
by Natacha Beck, Ms 17 Jul '12

17 Jul '12

Hello, I know that we can resume a recon-all command, if it's a cross-sectionnally process. In this case the command is: recon-all -make all -s subject But I had a power failure during a longitudinal study, when I try to execute : recon-all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2' That's why I would like to resume this command, that's why I tried : recon-all -make all -sd . -s 'Test_base_22' But I received this error : ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base <templateid> -tp <tpNid> ... \' So I tried this command: recon-all -make all -sd . -base 'Test_base_22' -tp 'OAS2_0001_MR1' -tp 'OAS2_0001_MR2' But I received the same error: Subject Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Current Stamp: freesurfer-Darwin-leopard-i686-stable-pub-v5.1.0 Subject 'Test_base_22': make all recon-all -s /Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22 -talairach -tal-check ERROR: It appears that this subject ID is an existing base/template from longitudinal processing (-base). Please make sure you pass all necessary flags. For example, if you are trying to re-run a -base: \' -base <templateid> -tp <tpNid> ... \' make: *** [/Users/****/tool_test/FreeSurfer/longi/restart/Test_base_22/mri/transforms/talairach.auto.xfm] Error 1 Somebody can help me and tell me which command I need to execute. Natacha

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