QDEC cannot but the information may be in the output folder. There should be a file called gammavar.mgh. This will be the standard variance (so take the square root)

On 12/21/2015 02:08 PM, John Anderson wrote:

Thanks you very much Doug, Please one more question. Is there any way in Qdec to get the stamdard error (SE) ? Bests, John *Sent:* Monday, December 21, 2015 at 11:43 AM *From:* "Douglas N Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Qdec visualization The correction for multiple comparisons is cluster-based. Each cluster gets a single number. In the display, all the vertices get that same number.

On 12/18/2015 03:17 PM, John Anderson wrote:

...

Hi Freesurfer experts, I am using Qdec in Freesurfer 5.3 to do some cortical thickness comparisons between two groups.

Before corrcting the results for multiple comparisons ( monte carlo simulation) the significant differnce between the groups is visualized as a range of color while after correcting for multiple copmparisons the color of the statistical map is usinform ( Attached) Is ther any way to visualze the results as a range of color after correcting the results for multiple comparsiosn

Thanks in advance for any advice Bests, John Anderson

Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419

---

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 greve@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 http://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

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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

it helps to see the error msg, but my guess is that you need to specify an mgh file, not a txt file. This will give you the voxel-wise stderr, not a standard error for the cluster (which does not make sense)

On 12/21/2015 02:38 PM, John Anderson wrote:

Hi Doug, Given that the standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation? I tried: mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong? Bests, John *Sent:* Monday, December 21, 2015 at 2:20 PM *From:* "Douglas N Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Qdec visualization QDEC cannot but the information may be in the output folder. There should be a file called gammavar.mgh. This will be the standard variance (so take the square root)

On 12/21/2015 02:08 PM, John Anderson wrote:

...

Thanks you very much Doug, Please one more question. Is there any way in Qdec to get the stamdard error (SE) ? Bests, John *Sent:* Monday, December 21, 2015 at 11:43 AM *From:* "Douglas N Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Qdec visualization The correction for multiple comparisons is cluster-based. Each cluster gets a single number. In the display, all the vertices get that same number.

On 12/18/2015 03:17 PM, John Anderson wrote:

...

Hi Freesurfer experts, I am using Qdec in Freesurfer 5.3 to do some cortical thickness comparisons between two groups.

Before corrcting the results for multiple comparisons ( monte carlo simulation) the significant differnce between the groups is visualized as a range of color while after correcting for multiple copmparisons the color of the statistical map is usinform ( Attached) Is ther any way to visualze the results as a range of color after correcting the results for multiple comparsiosn

Thanks in advance for any advice Bests, John Anderson

Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755 Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419

---

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 greve@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

http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

...

http://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

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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 http://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

why did you not use fscalc, eg,

fscalc var.mgh -sqrt -o stderr.mgh

On 12/21/2015 03:04 PM, John Anderson wrote:

Thanks Doug, I used the command "mris_calc gammavar.mgh sqrt" and the output was: _"Saving result to 'out.mgz' (type = MGH _)" *Then* I ran the command "mris_calc out.mgz stats" and the output was : Size [ 163842 ] Min@(index) [ 0.000000 (161385) ] Max@(index) [ 0.259395 (18208) ] Mean [ 0.097956 ] Std [ 0.040943 ] Sum [ 16049.365234 ] Prod [ 0.000000 ] In order to calculate the standard error is it fine if I use _*mris_calc *__*gammavar.mgh stats*_ the I divide the *Std* of gammavar.mgh by the square root of the sample size ( number of subjects included in the analysis)? Thanks a lot! *Sent:* Monday, December 21, 2015 at 2:44 PM *From:* "Douglas N Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Qdec visualization it helps to see the error msg, but my guess is that you need to specify an mgh file, not a txt file. This will give you the voxel-wise stderr, not a standard error for the cluster (which does not make sense)

On 12/21/2015 02:38 PM, John Anderson wrote:

...

Hi Doug, Given that the standard variance can be calculated using the command "mris_calc" and the flag "-sqrt" what is the correct command to do this calculation? I tried: mris_calc gammavar.mgz -sqrt output.txt but it didn't work. Kindly what I am doing wrong? Bests, John *Sent:* Monday, December 21, 2015 at 2:20 PM *From:* "Douglas N Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Qdec visualization QDEC cannot but the information may be in the output folder. There should be a file called gammavar.mgh. This will be the standard variance (so take the square root)

On 12/21/2015 02:08 PM, John Anderson wrote:

...

Thanks you very much Doug, Please one more question. Is there any way in Qdec to get the stamdard error (SE) ? Bests, John *Sent:* Monday, December 21, 2015 at 11:43 AM *From:* "Douglas N Greve" greve@nmr.mgh.harvard.edu *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Qdec visualization The correction for multiple comparisons is cluster-based. Each cluster gets a single number. In the display, all the vertices get that same number.

On 12/18/2015 03:17 PM, John Anderson wrote:

...

Hi Freesurfer experts, I am using Qdec in Freesurfer 5.3 to do some cortical thickness comparisons between two groups.

Before corrcting the results for multiple comparisons ( monte carlo simulation) the significant differnce between the groups is

visualized

...

...

...

as a range of color while after correcting for multiple copmparisons the color of the statistical map is usinform ( Attached) Is ther any way to visualze the results as a range of color after correcting the results for multiple comparsiosn

Thanks in advance for any advice Bests, John Anderson

Senior Research Associate Psychological and Brain Sciences Dept. Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH

03755

...

...

...

Phone: +1 (603) 646-9834 Fax: +1 (603) 646-1419

---

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 greve@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

http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

...

http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

...

http://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

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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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

http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html

...

http://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

-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@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 http://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