Re: [Freesurfer] QDEC question
Hello Dr Greve, Many thanks for replying to me. We are not including eTIV as a covariate. Since we did not find any correlation with the thickness. Kind regards, Sampada ___ Freesurfer mailing list 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.
[Freesurfer] Regarding: 3 groups and 1 covariate contrast
Dear freesurfer experts, I am trying to find group difference (thickness) among 3 groups (SCA1, SCA2, SCA3) taking in account one covariate (CAG levels). Will you please let me know if I need to use DODS or DOSS, though I am more interested in using DODS. I read the FSGD examples page ( https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf3G0V) and I made the fsgd file (One Factor/Three Levels), one Covariate (please see the attached fsgd file). Now, my problem is how to create the contrast file. I know with DODS Nregressors will be 6. How do I create the contrasts matrix to run the mri_glmfit command? I could create only three .mtx file, which are: 3 classes 1 variable contrast 1.mtx - diff SCA1 vs SCA2 1 -1 0 0 0 0 contrast 2.mtx - diff SCA1 vs SCA3 1 0 -1 0 0 0 contrast 3.mtx - diff SCA2 vs SCA3 0 1 -1 0 0 0 Will you please let me know what other three contrasts matrix I should add?I did go through the freesurfer forum and found this one query particularly related to the same problem I am having (http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg33172.html). Do I go by this contrasts matrix format which Stefania has come up with? Forever appreciative of all your efforts and time given to me. -- S ampada AIIMS, New Delhi g3v1.fsgd Description: Binary data ___ Freesurfer mailing list 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.
Re: [Freesurfer] bad registration using mri_vol2vol
I made the label in tkmedit, then i used label2v Sent from my iPhone On Jul 24, 2015, at 12:22 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I've lost track of what is going on here. How was lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz created? On 7/23/15 12:08 PM, Barbour, Tracy,M.D. wrote: Thank you Doug I tried the way you suggested and the registration actually looks worse. I also tried: mri_label2vol --subject fsaverage --label /autofs/cluster/maury/users/gcoombs/College_Risk/SUBJECTS_DIR_FS53/fsaverage_copy/label/$label.label --o $TARGET_DIR/tracy2_$label.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --temp /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz Is there a step that I am missing? This is for an amygdala functional ROI that was created in tkmedit and saved as a label. Tracy From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Monday, July 20, 2015 2:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] bad registration using mri_vol2vol where did lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz come from? It must be in the space of $SUBJECTS_DIR/fsaverage/mri/orig.mgz for that transform to work On 07/17/2015 02:43 PM, Barbour, Tracy,M.D. wrote: Hello, I'm trying to convert an ROI mask I created in MNI305 space to MNI152. After running MRI_vol2vol the registration looks off (too anterior). Here are my commands: mri_convert -ot nii lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.mgz lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii mri_vol2vol --mov /autofs/cluster/maury/users/gcoombs/College_Risk/fcMRI/N12Trio_avg152T1.nii.gz --targ lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii --inv --interp nearest --reg $FREESURFER_HOME/average/mni152.register.dat --o new_lh.amyg.faceaw_func.anatconstr.p05.5.3CRFH.n70.nii.gz Any ideas why the registration is off? Tracy ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list 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.
Re: [Freesurfer] hello freesurfer developer~
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 fis...@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 naniy...@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 naniy...@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 fis...@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 fis...@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,
Re: [Freesurfer] hello freesurfer developer~
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 fis...@nmr.mgh.harvard.edu mailto:fis...@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 naniy...@gmail.com mailto:naniy...@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 naniy...@gmail.com mailto:naniy...@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 fis...@nmr.mgh.harvard.edu mailto:fis...@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 fis...@nmr.mgh.harvard.edu mailto:fis...@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
Re: [Freesurfer] hello freesurfer developer~
Maybe Zeke or Ruopeng know? On Jul 26, 2015, at 5:17 PM, A-reum Min naniy...@gmail.com 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 fis...@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 naniy...@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 naniy...@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 fis...@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 fis...@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
Re: [Freesurfer] hello freesurfer developer~
Hello bruce I solve this problem(12.png) Thank you 2015-07-27 13:03 GMT+09:00 dgw dgwake...@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 fis...@nmr.mgh.harvard.edu mailto:fis...@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 naniy...@gmail.com mailto:naniy...@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 naniy...@gmail.com mailto:naniy...@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 fis...@nmr.mgh.harvard.edu mailto:fis...@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 fis...@nmr.mgh.harvard.edu mailto:fis...@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
