[Freesurfer] Design Matrix Creation
Freesurfer Support, Thank you for your support with my previous line of questions regarding design matrix creation. I have manually created another design matrix and want to ensure that I designed it correctly. An example of my FSGD file is as follows below: Class SITE 1-Male-Control Class SITE 1-Male-PATIENT Class SITE 1-Female-Control Class SITE 1-Female-PATIENT Class SITE 2-Male-Control Class SITE 2-Male-PATIENT Class SITE 2-Female-Control Class SITE 2-Female-PATIENT Class SITE 3-Male-Control Class SITE 3-Male-PATIENT Class SITE 3-Female-Control Class SITE 3-Female-PATIENT Class SITE 4-Male-Control Class SITE 4-Male-PATIENT Class SITE 4-Female-Control Class SITE 4-Female-PATIENT Variables age_at_scan total_intracranial_volume study site levels = 1, 2, 3, 4 gender levels = Male, Female diagnosis levels = PATIENT, Control age_at_scan = covariate age total_intracranial_volume = covariate total intracranial volume What I would ideally like to do is: 1) Take into account offset differences amongst diagnosis, gender, and study site. 2) Allowing a difference in age slope, and total intracranial volume slope amongst the diagnosis and gender levels. 3) Modeling the age slope and total intracranial volume slope as the same for the study site levels. Let's image that the first participant is from site 1, Male, and control, and is 12 and has a TIV of 30,000. The second participant is from site 2, Female, and PATIENT, and is 14, and has a TIV of 25,000. My understanding of the design matrix would be as follows: 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 3 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000 -Tim >Yes, create your matrix manually. > >Those matrix lines are not quite right. The ages are in the correct >column, but you need a 1 somewhere in columns 1-8 to indicate the class >(ie, site/dx) that the subject is in. On 05/26/2016 12:57 PM, Timothy Hendrickson wrote: > Hi Doug, > > Thank you for such a prompt response. Just to be clear you are > recommending that I manually create the matrix file right? > > If so I want to ensure that I am understanding how to design the > matrix file properly. > > Let's imagine that the first participant is a control and is 13 and > the second is a patient and is 15. My understanding is that the matrix > file would be as follows: > 0 0 0 0 0 0 0 0 13 0 > 0 0 0 0 0 0 0 0 0 15. > > -Tim > Previous correspondences are below: > > You'll need a regressor for each of the 8 classes you describe below. > You can use mri_glmfit to generate this (Xg.dat file) > You'll need two more regressors for age, one for each diagnosis. If a > subject (ie, row) is a control then the two values will be AGE 0. If the > subject of the row is a patient, then the two values will be 0 AGE. You > can then set up a Controls-Patients age (ie, interaction between dx and > age) contrast like > [0 0 0 0 0 0 0 0 1 -1] > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote: > > > > Freesurfer Support, > > > > I'd like to create a design matrix for a group analysis outside of the > > DODS and DOSS models. I understand that in order to do this the -X > > flag must be used. However, I have been unable to find examples of how > > to do this. > > > > I am hoping to reveal a difference in thickness or gyrification > > amongst a clinical population. The data set contains two factors: > > diagnosis, and study site and one covariate: age. Diagnosis has two > > levels: controls, and patients. Study site has four levels, one level > > for each location the data has been collected from. > > > > What I would ideally like to do is: > > > > 1) Take into account offset differences amongst diagnosis and study site. > > > > 2) Allowing a difference in age slope amongst the diagnosis levels > > > > 3) Modeling the age slope as the same for the study site levels > > > > My FSGD file is designed as follows > > > > Class SITE 1-Control > > Class SITE 1-PATIENT > > Class SITE 2-Control > > Class SITE 2-PATIENT > > Class SITE 3-Control > > Class SITE 3-PATIENT > > Class SITE 4-Control > > Class SITE 4-PATIENT > > Variables age_at_scan > > > > study site levels = 1,2,3 and 4 > > diagnosis levels = PATIENT and Control > > age_at_scan = covariate age > > > > Any advice would be greatly appreciated. > > > > Respectfully, > > > > Tim > > > > -- > > Timothy Hendrickson > > Department of Psychiatry > > University of Minnesota > > Mobile: 507-259-3434 (texts okay) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin
[Freesurfer] LGI Summary Statistics
Freesurfer Support, I have seen previous message threads on extracting LGI measurements across ROIs, however I have yet to find anything which would provide a summary LGI across an entire hemsphere. Other measurements like cortical thickness have a measurement like this. Is there a measurement like this for LGI? If I take the mean of all of the ROIs would that be equivalent to a hemispheric LGI measure? Thanks! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Design Matrix Creation
Hi Doug, I just wanted to make sure that we were on the same page. I may have been a little unclear in what I would ideally like to do. For #2 what I would like to do is take into account age slopes and total intracranial slopes for gender, and age slopes and total intracranial slopes for diagnosis. I was not implying that I wanted diagnosis and gender to interact. Assuming that you understood this previously could you please explain why you would model the matrix this way? I do not fully understand. Respectfully, -Tim >I did not get the same matrix. Here's how I would do it >Columns 1-16 model the intercepts for all your classes >Columns 17-20 model the ages for your gender-x-diagnosis subclasses >Columns 21-24 model the ICV for your gender-x-diagnosis subclasses On 07/06/2016 02:04 PM, Timothy Hendrickson wrote: > Freesurfer Support, > > Thank you for your support with my previous line of questions regarding > design matrix creation. > I have manually created another design matrix and want to ensure that I > designed it correctly. > > An example of my FSGD file is as follows below: > Class SITE 1-Male-Control > Class SITE 1-Male-PATIENT > Class SITE 1-Female-Control > Class SITE 1-Female-PATIENT > Class SITE 2-Male-Control > Class SITE 2-Male-PATIENT > Class SITE 2-Female-Control > Class SITE 2-Female-PATIENT > Class SITE 3-Male-Control > Class SITE 3-Male-PATIENT > Class SITE 3-Female-Control > Class SITE 3-Female-PATIENT > Class SITE 4-Male-Control > Class SITE 4-Male-PATIENT > Class SITE 4-Female-Control > Class SITE 4-Female-PATIENT > Variables age_at_scan total_intracranial_volume > study site levels = 1, 2, 3, 4 > gender levels = Male, Female > diagnosis levels = PATIENT, Control > age_at_scan = covariate age > total_intracranial_volume = covariate total intracranial volume > > What I would ideally like to do is: > > 1) Take into account offset differences amongst diagnosis, gender, and study > site. > > 2) Allowing a difference in age slope, and total intracranial volume slope > amongst the diagnosis and gender levels. > > 3) Modeling the age slope and total intracranial volume slope as the same for > the study site levels. > Let's image that the first participant is from site 1, Male, and control, and > is 12 and has a TIV of 30,000. > The second participant is from site 2, Female, and PATIENT, and is 14, and > has a TIV of 25,000. > My understanding of the design matrix would be as follows: > 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 0 0 0 3 0 0 0 > 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 14 0 0 0 25000 > -Tim > > >Yes, create your matrix manually. > > > >Those matrix lines are not quite right. The ages are in the correct > >column, but you need a 1 somewhere in columns 1-8 to indicate the class > >(ie, site/dx) that the subject is in. > On 05/26/2016 12:57 PM, Timothy Hendrickson wrote: > > Hi Doug, > > > > Thank you for such a prompt response. Just to be clear you are > > recommending that I manually create the matrix file right? > > > > If so I want to ensure that I am understanding how to design the > > matrix file properly. > > > > Let's imagine that the first participant is a control and is 13 and > > the second is a patient and is 15. My understanding is that the matrix > > file would be as follows: > > 0 0 0 0 0 0 0 0 13 0 > > 0 0 0 0 0 0 0 0 0 15. > > > > -Tim > > Previous correspondences are below: > > > > You'll need a regressor for each of the 8 classes you describe below. > > You can use mri_glmfit to generate this (Xg.dat file) > > You'll need two more regressors for age, one for each diagnosis. If a > > subject (ie, row) is a control then the two values will be AGE 0. If the > > subject of the row is a patient, then the two values will be 0 AGE. You > > can then set up a Controls-Patients age (ie, interaction between dx and > > age) contrast like > > [0 0 0 0 0 0 0 0 1 -1] > > On 05/24/2016 02:30 PM, Timothy Hendrickson wrote: > > > > > > Freesurfer Support, > > > > > > I'd like to create a design matrix for a group analysis outside of the > > > DODS and DOSS models. I understand that in order to do this the -X > > > flag must be used. However, I have been unable to find examples of how > > > to do this. > > > > > > I am hoping to reveal a difference in thickness or gyrification > > > amongst a clinical population. The data set contains two factors: > > > diagnosis, and study site and one covariate: age. Diagnosis has two > > > levels: controls, and patients. Study site has four levels, on
[Freesurfer] Performing GLM within a Mask Specified by Another GLM
Freesurfer Support, Here is what I would like to do: I have run a GLM on the entire cortex to determine whether there are significant differences in LGI between patients and controls. I then would like run a different GLM just with the clusters outputted from the previous GLM. It would seem that the best thing to do is to set a mask representing the clusters from the first GLM and then run the second GLM on the mask. Is this a reasonable thing to do? What steps/commands would I perform in order to do something like this? Respectfully, -Tim Hendrickson Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Cluster Forming Threshold
Freesurfer Experts, I am currently using a Monte Carlo Z-Simulation to perform multiple comparisons on a data set. I have played around with various cluster forming threshold and cluster wise thresholds. I have no idea what would be considered "too liberal" or "too conservative" of thresholds and I have not found much literature that decimates this either. Are there any general best practices I should follow when determining these thresholds? Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] mri_glmfit --pvr Assistance
FreeSurfer Experts, I have a data set which comprises one group and the co-variate IQ. I would like to correlate this data set with the dependent measure LGI. I originally performed this in QDEC, however I read elsewhere that a vertex-by-vertex correlation cannot be done in QDEC. Further, I read that it must be done via command line with mri_glmfit and the --pvr flag. I am confused as to what sort of file I should input into the --pvr flag (do I run a separate analysis?, etc). Any advice would be extremely helpful. Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Two Stage Longitudinal Model
FreeSurfer Experts, Hello I am attempting to perform a two stage longitudinal analysis. My entire data set has two time points for each participant. I understand that the subject order in the FSGD file should correspond with the QDEC file run through long_mris_slopes. In my case the FSGD file has half as many inputs as the QDEC file. My question is would I take the covariates from TP1 and TP2 and take the average to input into the FSGD file? If that is the case is there anything wrong with performing the long_qdec_table --qdec "qdec.table.dat --cross --out "cross.qdec.table.dat" command and using that co-variate data to input into the FSGD file? Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Two Stage Longitudinal Model
Hi Martin, Thank you for your reply. I am glad to hear that I am doing that correctly. I am running into an error when I attempted to run my GLM. I have looked at my fsgd and qdec files for errors, however I cannot seem to find anything. The error is in the attached .txt file named illCondMatrix_twoStage_years_10_31_16.txt. Additionally I've included my fsgd file for stage two and my qdec file for stage one. Any assistance would be extremely helpful, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) Normalized matrix condition is 129299 Design matrix -- 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.995; 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.010 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.050; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000 0.000 0.555 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 1.010 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 1.005 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.010 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.005; 0.000 0.000 1.000 0.000 0.000 0.000 1.035 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.495 0.000; 1.000 0.000 0.000 0.000 0.995 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 1.000 0.000 0.000; 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.985 0.000 0.000; 1.000 0.000 0.000 0.000 0.990 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.980; 0.000 1.000 0.000 0.000 0.000 0.980 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000; 0.000 1.000 0.000 0.000 0.000 0.990 0.000 0.000; 1.000 0.000 0.000 0.000 0.990 0.000 0.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.990; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.990; 1.000 0.000 0.000 0.000 0.985 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.985 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.010 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.985 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.000 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.995 0.000; 1.000 0.000 0.000 0.000 0.995 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 1.450 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.990 0.000; 0.000 1.000 0.000 0.000 0.000 0.995 0.000 0.000; 1.000 0.000 0.000 0.000 0.995 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.995 0.000; ERROR: matrix is ill-conditioned or badly scaled, condno = 129299 Possible problem with experimental design: Check for duplicate entries and/or lack of range of continuous variables within a class. If you seek help with this problem, make sure to send: 1. Your command line: mri_glmfit --glmdir rh.UMN.gender.group.Years.thickness.fwhm10.twoStage.glmdir --fsgd twoStageLongitudinal_BaseUMN_Gender_Group_Years.fsgd dods --y rh.testretest.thickness-pc1.stack.fwhm10.mgh --C DiffDiagnosis_ControlMore_AcctGender_AcctYearDiff_twoStage_10_25_16.mtx --C DiffDiagnosis_ControlMore_AcctGender_YearDiffSlope_twoStage_10_25_16.mtx --C DiffGender_MaleMore_AcctGroup_AcctYearDiff_twoStage_10_25_16.mtx --C DiffGender_MaleMore_AcctGroup_YearDiffSlope_twoStage_10_25_16.mtx --C YearDiff_AcctGender_AcctSite_twoStage_10_25_16.mtx --label rh.testretest.fsaverage.cortex.label --surf fsaverage rh 2. The FSGD file (if using one) 3. And the design matrix above twoStageLongitudinal_BaseUMN_Gender_Group_Years.fsgd Description: Binary data twoStage_UMN_Group_Sex_Years.table.dat 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.
[Freesurfer] Longitudinal Stream on HCP Data
Hi Freesurfer/HCP experts, I am curious if there is a way to incorporate HCP data (i.e. myelin maps) into the FreeSurfer processing stream. Matthew Glasser mentioned in a post on the HCP mailing list about a month back that this is being actively worked on by FreeSurfer: http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html. <http://www.mail-archive.com/hcp-users@humanconnectome.org/msg03477.html> Are there any workflows or development versions that I can download in order to perform something like this. Respectfully, -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Fwd: [HCP-Users] HCP to FreeSurfer Resampling
FreeSurfer experts, I am attempting to resample HCP data into FreeSurfer space with the following how to document: https://wiki.humanconnectome. org/display/PublicData/HCP+Users+FAQ. <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ> I believe I have resampled the GIFTI file into fs_average space, however I am running to problems visualizing it in freeview or tksurfer. Please see the error message in the forwarded message below? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) -- Forwarded message -- From: Timothy Hendrickson Date: Tue, Nov 8, 2016 at 8:51 AM Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling To: Timothy Coalson Cc: "hcp-us...@humanconnectome.org" Hi Tim, Thank you for taking a look at my script, I really appreciate it. I am now running into another problem. After re-sampling into fs_average space I am attempting to visualize that file as an overlay in tksurfer or freeview (freesurfer visualization tools) however I receive the following error: *mriseadGIFTIfile: mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I know that freesurfer can handle GIFTI file so that is not the problem. I wonder if the GIFTI file was created incorrectly... Any advice? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Longitudinal Stream on HCP Data
Aww thank you for clarifying Michael. I definitely misread Matthew's post. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Cluster Color
It seems that this message has been ignored. I really do need an answer on this. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ 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] Fwd: [HCP-Users] HCP to FreeSurfer Resampling
Just following up on the message below. Respectfully, -Tim FreeSurfer experts, I am attempting to resample HCP data into FreeSurfer space with the following how to document: https://wiki.humanconnectome. org/display/PublicData/HCP+Users+FAQ. <https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ> I believe I have resampled the GIFTI file into fs_average space, however I am running to problems visualizing it in freeview or tksurfer. Please see the error message in the forwarded message below? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) -- Forwarded message -- From: Timothy Hendrickson Date: Tue, Nov 8, 2016 at 8:51 AM Subject: Re: [HCP-Users] HCP to FreeSurfer Resampling To: Timothy Coalson Cc: "hcp-us...@humanconnectome.org" Hi Tim, Thank you for taking a look at my script, I really appreciate it. I am now running into another problem. After re-sampling into fs_average space I am attempting to visualize that file as an overlay in tksurfer or freeview (freesurfer visualization tools) however I receive the following error: *mriseadGIFTIfile: mris is NULL! found when parsing file rh.43242.32k_TJH_fsavg.func.gii*. I know that freesurfer can handle GIFTI file so that is not the problem. I wonder if the GIFTI file was created incorrectly... Any advice? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ______ Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ 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] Trouble with Two Stage Longitudinal Analysis
FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I belive I have cross-checked my qdec, fsgd, design matrix, and contrast files and they all match so I do not think the problem is a mismatch. I am wondering if I made some sort of mistake in my script design or design matrix creation... Anyway here is the command line input: mri_glmfit --glmdir lh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat --y lh.testretest.thickness-pc1.stack.fwhm10.mgh --C age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx --label lh.testretest.fsaverage.cortex.label --surf fsaverage lh The error message is attached within file AllSite_twoStageLongitudinal_DsgnMtxErr.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix -- 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.600 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.800 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.200 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.295 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.800 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.495 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.095 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.895 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.665 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.745 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.995; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.740; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.265 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.240 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.415 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.835 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.240 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.835 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.825 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1
[Freesurfer] Trouble with Two Stage Longitudinal Analysis
I was able to figure out my design matrix issue. I had not originally appreciated that there were no data sets from a particular class. Thanks! -Tim FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I belive I have cross-checked my qdec, fsgd, design matrix, and contrast files and they all match so I do not think the problem is a mismatch. I am wondering if I made some sort of mistake in my script design or design matrix creation... Anyway here is the command line input: mri_glmfit --glmdir lh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat --y lh.testretest.thickness-pc1.stack.fwhm10.mgh --C age_AcctGroup_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_twoStage.DOSSDS.mtx --C DiffDiagnosis_ControlMore_AgeSlope_AcctSite_AcctGender_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AcctSite_AcctDiagnosis_AcctAge_twoStage.DOSSDS.mtx --C DiffGender_MaleMore_AgeSlope_AcctSite_AcctDiagnosis_twoStage.DOSSDS.mtx --label lh.testretest.fsaverage.cortex.label --surf fsaverage lh The error message is attached within file AllSite_twoStageLongitudinal_DsgnMtxErr.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix -- 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.600 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 13.800 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.200 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 16.295 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 17.800 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 12.495 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 11.095 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 15.895 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.665 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.745 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 12.500 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.995; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.740; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.265 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.240 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 13.415 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.835 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 14.240 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 11.835 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 16.825 0.000 0.000; 0.000 0.000 0.000
[Freesurfer] Poorly Designed Matrix Two Stage Longitudinal Model
FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I'm curious, I've used the same format of design matrix on cross sectional without problem. Anyway here is the command line input: mri_glmfit --glmdir rh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir \ --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \ --y rh.testretest.thickness-spc.stack.fwhm10.mgh \ --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_pairedAnalysis.DOSSDS.mtx \ --label rh.testretest.fsaverage.cortex.label \ --surf fsaverage rh The error message is attached within file error_designMtx_12_19_16.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. Any help would be extremely beneficial. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix -- 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.878; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -2.325; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.967; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.552 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.121 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.588 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.101 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -2.205; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.775 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.316 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.590 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.093 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.880 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -2.131 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.632 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.908 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.447 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.635 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.859 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.588 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.858 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.051; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.641 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.217; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
[Freesurfer] Poorly Designed Matrix Two Stage Longitudinal Model
Just following up on the message below. I would appreciate a comment on this issue. -Tim FreeSurfer experts, I am attempting to use the two stage model for longitudinal analysis, however I keep receiving an error message that my design matrix is poorly scaled. I'm curious, I've used the same format of design matrix on cross sectional without problem. Anyway here is the command line input: mri_glmfit --glmdir rh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir \ --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \ --y rh.testretest.thickness-spc.stack.fwhm10.mgh \ --C DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_pairedAnalysis.DOSSDS.mtx \ --label rh.testretest.fsaverage.cortex.label \ --surf fsaverage rh The error message is attached within file error_designMtx_12_19_16.txt Additionally I've included my analysis script, all timepoint qdec file, temporal average qdec file, fsgd file, and design matrix. Any help would be extremely beneficial. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) Design matrix -- 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.878; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -2.325; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.967; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.552 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.121 0.000 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.588 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.101 0.000; 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -2.205; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.775 0.000 0.000 0.000; 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.316 0.000 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.590 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.093 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.880 0.000 0.000; 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -2.131 0.000 0.000; 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.632 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.908 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.447 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.635 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.859 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.588 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.858 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -0.051; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 -1.641 0.000 0.000 0.000; 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.217; 0.000 0.000
Re: [Freesurfer] Poorly Designed Matrix Two Stage Longitudinal Model
Doug, That did it! Thank you so much for your help! -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) On Wed, Dec 21, 2016 at 12:47 PM, Douglas N Greve wrote: > your 10th column is all 0s > > > On 12/21/2016 01:26 PM, Timothy Hendrickson wrote: > > Just following up on the message below. I would appreciate a comment on > this issue. > > > > -Tim > > FreeSurfer experts, > > > > I am attempting to use the two stage model for longitudinal analysis, > > however I keep receiving an error message that my design matrix is poorly > > scaled. > > I'm curious, I've used the same format of design matrix on cross > > sectional without problem. > > Anyway here is the command line input: > > > > mri_glmfit --glmdir > > rh.AllSite.gender.group.Age.thickness.fwhm10.twoStage.glmdir \ > > --X DOSSDS.twoStage_AllSite_Gender_Group_Age.dat \ > > --y rh.testretest.thickness-spc.stack.fwhm10.mgh \ > > --C > > DiffDiagnosis_ControlMore_AcctSite_AcctGender_AcctAge_ > pairedAnalysis.DOSSDS.mtx > > \ > > --label rh.testretest.fsaverage.cortex.label \ > > --surf fsaverage rh > > > > The error message is attached within file > > error_designMtx_12_19_16.txt > > > > Additionally I've included my analysis script, all timepoint qdec file, > > temporal average qdec file, fsgd file, and design matrix. > > Any help would be extremely beneficial. > > > > -Tim > > > > Timothy Hendrickson > > Department of Psychiatry > > University of Minnesota > > Office: 612-624-6441 > > Mobile: 507-259-3434 (texts okay) > > Design matrix -- > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > -1.878; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > -2.325; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > -1.967; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.552 > 0.000; > > 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 -0.121 0.000 0.000 > 0.000; > > 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.588 0.000 > 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 1.101 > 0.000; > > 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > -2.205; > > 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.775 0.000 0.000 > 0.000; > > 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 1.316 0.000 0.000 > 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -0.590 > 0.000; > > 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.093 0.000 > 0.000; > > 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -1.880 0.000 > 0.000; > > 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 -2.131 0.000 > 0.000; > > 0.000 0.000 1.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.632 > 0.000; > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 > > 0.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 0.908 > 0.000; > > 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 > 0.000 >
[Freesurfer] Cluster Color
Free Surfer Support, I have been using the command line version for group analysis since my data set has too many factors for QDEC. There are a few things that I enjoy about QDEC that I wish I could incorporate into the command line. 1) In QDEC the cluster color is not set arbitrarily, but rather based on significance. Is there any way to have the cluster color be set based on significance at command line? Is there a way to restrict the available colors that the clusters can be set as? Occasionally, cluster colors are a very similar color to the inflated underlay making it difficult to determine the outline of said cluster. 2) In QDEC one is able to visualize a scatter plot for a particular cluster. Is there any way to do this via the command line option? Thank you, -Tim Hendrickson -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Cluster Color
I'm just following up on this e-mail. I have not heard anything yet. -Tim On Mon, May 9, 2016 at 3:16 PM, Timothy Hendrickson wrote: > Free Surfer Support, > > I have been using the command line version for group analysis since my > data set has too many factors for QDEC. > > There are a few things that I enjoy about QDEC that I wish I could > incorporate into the command line. > > 1) In QDEC the cluster color is not set arbitrarily, but rather based on > significance. > > Is there any way to have the cluster color be set based on significance at > command line? > > Is there a way to restrict the available colors that the clusters can be > set as? > Occasionally, cluster colors are a very similar color to the inflated > underlay making it difficult to determine the outline of said cluster. > > 2) In QDEC one is able to visualize a scatter plot for a particular > cluster. Is there any way to do this via the command line option? > > Thank you, > > -Tim Hendrickson > > -- > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Mobile: 507-259-3434 (texts okay) > -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Design Matrix Creation
Freesurfer Support, I'd like to create a design matrix for a group analysis outside of the DODS and DOSS models. I understand that in order to do this the -X flag must be used. However, I have been unable to find examples of how to do this. I am hoping to reveal a difference in thickness or gyrification amongst a clinical population. The data set contains two factors: diagnosis, and study site and one covariate: age. Diagnosis has two levels: controls, and patients. Study site has four levels, one level for each location the data has been collected from. What I would ideally like to do is: 1) Take into account offset differences amongst diagnosis and study site. 2) Allowing a difference in age slope amongst the diagnosis levels 3) Modeling the age slope as the same for the study site levels My FSGD file is designed as follows Class SITE 1-Control Class SITE 1-PATIENT Class SITE 2-Control Class SITE 2-PATIENT Class SITE 3-Control Class SITE 3-PATIENT Class SITE 4-Control Class SITE 4-PATIENT Variables age_at_scan study site levels = 1,2,3 and 4 diagnosis levels = PATIENT and Control age_at_scan = covariate age Any advice would be greatly appreciated. Respectfully, Tim -- Timothy Hendrickson Department of Psychiatry University of Minnesota Mobile: 507-259-3434 (texts okay) ___ 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] Design Matrix Creation
Hi Doug, Thank you for such a prompt response. Just to be clear you are recommending that I manually create the matrix file right? If so I want to ensure that I am understanding how to design the matrix file properly. Let's imagine that the first participant is a control and is 13 and the second is a patient and is 15. My understanding is that the matrix file would be as follows: 0 0 0 0 0 0 0 0 13 0 0 0 0 0 0 0 0 0 0 15. -Tim Previous correspondences are below: You'll need a regressor for each of the 8 classes you describe below. You can use mri_glmfit to generate this (Xg.dat file) You'll need two more regressors for age, one for each diagnosis. If a subject (ie, row) is a control then the two values will be AGE 0. If the subject of the row is a patient, then the two values will be 0 AGE. You can then set up a Controls-Patients age (ie, interaction between dx and age) contrast like [0 0 0 0 0 0 0 0 1 -1] On 05/24/2016 02:30 PM, Timothy Hendrickson wrote: > > Freesurfer Support, > > I'd like to create a design matrix for a group analysis outside of the > DODS and DOSS models. I understand that in order to do this the -X > flag must be used. However, I have been unable to find examples of how > to do this. > > I am hoping to reveal a difference in thickness or gyrification > amongst a clinical population. The data set contains two factors: > diagnosis, and study site and one covariate: age. Diagnosis has two > levels: controls, and patients. Study site has four levels, one level > for each location the data has been collected from. > > What I would ideally like to do is: > > 1) Take into account offset differences amongst diagnosis and study site. > > 2) Allowing a difference in age slope amongst the diagnosis levels > > 3) Modeling the age slope as the same for the study site levels > > My FSGD file is designed as follows > > Class SITE 1-Control > Class SITE 1-PATIENT > Class SITE 2-Control > Class SITE 2-PATIENT > Class SITE 3-Control > Class SITE 3-PATIENT > Class SITE 4-Control > Class SITE 4-PATIENT > Variables age_at_scan > > study site levels = 1,2,3 and 4 > diagnosis levels = PATIENT and Control > age_at_scan = covariate age > > Any advice would be greatly appreciated. > > Respectfully, > > Tim > > -- > Timothy Hendrickson > Department of Psychiatry > University of Minnesota > Mobile: 507-259-3434 (texts okay) > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR centergr...@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/filedrop2www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 athttp://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. On Tue, May 24, 2016 at 1:30 PM, Timothy Hendrickson wrote: > > Freesurfer Support, > > I'd like to create a design matrix for a group analysis outside of the > DODS and DOSS models. I understand that in order to do this the -X flag > must be used. However, I have been unable to find examples of how to do > this. > > I am hoping to reveal a difference in thickness or gyrification amongst a > clinical population. The data set contains two factors: diagnosis, and > study site and one covariate: age. Diagnosis has two levels: controls, and > patients. Study site has four levels, one level for each location the data > has been collected from. > > What I would ideally like to do is: > > 1) Take into account offset differences amongst diagnosis and study site. > > 2) Allowing a difference in age slope amongst the diagnosis levels > > 3) Modeling the age slope as the same for the study site levels > > My FSGD file is designed as follows > > Class SITE 1-Control > Class SITE 1-PATIENT > Class SITE 2-Control > Class SITE 2-PATIENT > Class SITE 3-Control > Class SITE 3-PATIENT > Class SITE 4-Control > Class SITE 4-PATIENT > Variables age_at_scan > > study site levels = 1,2,3 and 4 > diagnosis levels = PATIENT
[Freesurfer] Continuous co-variate by continuous co-variate interaction effects
Freesurfer experts, I have created a design matrix in order to test for whether there is an interaction effect between two continuous co-variates controlling for a categorical variable. So I have one categorical variable with two levels, and two continuous co-variates. My design matrix is as follows: 0 0 1 1 0 0 0 0 0 0 1 1 Is this correct? -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Bioinformatics and Computational Biology M.S. Candidate Office: 612-624-6441 Mobile: 507-259-3434 (texts okay) ___ 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] Continuous co-variate by continuous co-variate interaction effects
Hi Doug, Yes thank you this was my contrast matrix, not my design matrix. I've taken your advice by multiplying the co-variates together. Thanks for the help! -Tim ___ 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] mri_convert
External Email - Use Caution Hello, I am working on implementing third party designed code which runs freesurfer via the containerization tool docker. This code runs fine within docker so that it is not the problem. I am attempting to run this same code with a tool named udocker which is a tool that emulates a docker environment but does not require root user privileges in order to do so. Anyway long story short when I attempt to run the udocker container of freesurfer 5.3.0-HCP with the default backend (PRoot) I receive a mmap error with mri_convert which reads: PROT_EXEC | PROT_WRITE. I am able to work around this error in certain instances, but that is not important here. What is important is that when I run a udocker container with freesurfer 6 mri_convert runs without issue. My two questions are: 1) What differences exist between mri_convert between freesurfer 6 and 5.3.0 - HCP 2) Is there any way that I can download/install the newer version of mri_convert used for freesurfer 6 within 5.3.0 - HCP? -Tim Timothy Hendrickson Neuroimaging Analyst/Staff Scientist University of Minnesota Informatics Institute University of Minnesota Bioinformatics M.S. Candidate Office: 612-624-0783 Mobile: 507-259-3434 (texts okay) ___ 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] TRACUAL eddy_correct Usage
External Email - Use Caution Hello, I notice that within TRACULA 6.0 that eddy_correct is used for the eddy current correction. This is an older tool as compared to eddy, is there a reason that eddy_correct is still used? Have you done cross comparisons between eddy_correct and eddy? If so did you find much difference in eddy current corrections? Thanks! -Tim ___ 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.
